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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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2
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Dudka W, Salo VT, Mahamid J. Zooming into lipid droplet biology through the lens of electron microscopy. FEBS Lett 2024; 598:1127-1142. [PMID: 38726814 DOI: 10.1002/1873-3468.14899] [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: 01/26/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Electron microscopy (EM), in its various flavors, has significantly contributed to our understanding of lipid droplets (LD) as central organelles in cellular metabolism. For example, EM has illuminated that LDs, in contrast to all other cellular organelles, are uniquely enclosed by a single phospholipid monolayer, revealed the architecture of LD contact sites with different organelles, and provided near-atomic resolution maps of key enzymes that regulate neutral lipid biosynthesis and LD biogenesis. In this review, we first provide a brief history of pivotal findings in LD biology unveiled through the lens of an electron microscope. We describe the main EM techniques used in the context of LD research and discuss their current capabilities and limitations, thereby providing a foundation for utilizing suitable EM methodology to address LD-related questions with sufficient level of structural preservation, detail, and resolution. Finally, we highlight examples where EM has recently been and is expected to be instrumental in expanding the frontiers of LD biology.
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Affiliation(s)
- Wioleta Dudka
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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3
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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4
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Kroeger B, Manning SA, Fonseka Y, Oorschot V, Crawford SA, Ramm G, Harvey KF. Basal spot junctions of Drosophila epithelial tissues respond to morphogenetic forces and regulate Hippo signaling. Dev Cell 2024; 59:262-279.e6. [PMID: 38134928 DOI: 10.1016/j.devcel.2023.11.024] [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: 08/03/2022] [Revised: 09/08/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Organ size is controlled by numerous factors including mechanical forces, which are mediated in part by the Hippo pathway. In growing Drosophila epithelial tissues, cytoskeletal tension influences Hippo signaling by modulating the localization of key pathway proteins to different apical domains. Here, we discovered a Hippo signaling hub at basal spot junctions, which form at the basal-most point of the lateral membranes and resemble adherens junctions in protein composition. Basal spot junctions recruit the central kinase Warts via Ajuba and E-cadherin, which prevent Warts activation by segregating it from upstream Hippo pathway proteins. Basal spot junctions are prominent when tissues undergo morphogenesis and are highly sensitive to fluctuations in cytoskeletal tension. They are distinct from focal adhesions, but the latter profoundly influences basal spot junction abundance by modulating the basal-medial actomyosin network and tension experienced by spot junctions. Thus, basal spot junctions couple morphogenetic forces to Hippo pathway activity and organ growth.
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Affiliation(s)
- Benjamin Kroeger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia; Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Samuel A Manning
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia; Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Yoshana Fonseka
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Viola Oorschot
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Melbourne, VIC 3168, Australia
| | - Simon A Crawford
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Melbourne, VIC 3168, Australia
| | - Georg Ramm
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Melbourne, VIC 3168, Australia
| | - Kieran F Harvey
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia; Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia.
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5
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Ariotti N. Investigating Epidermal Growth Factor Receptor Trafficking with High-Resolution Enzymatic Protein-Tagging and Transmission Electron Microscopy. Methods Mol Biol 2024; 2800:75-87. [PMID: 38709479 DOI: 10.1007/978-1-0716-3834-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Enzymatic ascorbate peroxidase (APEX) tagging allows for high-resolution, three-dimensional protein distribution analyses in cells and tissues. This chapter describes the application of APEX-tagging to visualize the trafficking of the epidermal growth factor receptor (EGFR) during epidermal growth factor-mediated receptor activation. Here, we describe the preparation of cells, methods to validate the stimulation of the EGFR, and visualization of the APEX-resolved distribution of the EGFR in the transmission electron microscope.
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Affiliation(s)
- Nicholas Ariotti
- Institute for Molecular Bioscience, Centre for Cell Biology of Chronic Disease, The University of Queensland, St Lucia, Brisbane, Australia.
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6
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Martins-Marques T, Witschas K, Ribeiro I, Zuzarte M, Catarino S, Ribeiro-Rodrigues T, Caramelo F, Aasen T, Carreira IM, Goncalves L, Leybaert L, Girao H. Cx43 can form functional channels at the nuclear envelope and modulate gene expression in cardiac cells. Open Biol 2023; 13:230258. [PMID: 37907090 PMCID: PMC10645070 DOI: 10.1098/rsob.230258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023] Open
Abstract
Classically associated with gap junction-mediated intercellular communication, connexin43 (Cx43) is increasingly recognized to possess non-canonical biological functions, including gene expression regulation. However, the mechanisms governing the localization and role played by Cx43 in the nucleus, namely in transcription modulation, remain unknown. Using comprehensive and complementary approaches encompassing biochemical assays, super-resolution and immunogold transmission electron microscopy, we demonstrate that Cx43 localizes to the nuclear envelope of different cell types and in cardiac tissue. We show that translocation of Cx43 to the nucleus relies on Importin-β, and that Cx43 significantly impacts the cellular transcriptome, likely by interacting with transcriptional regulators. In vitro patch-clamp recordings from HEK293 and adult primary cardiomyocytes demonstrate that Cx43 forms active channels at the nuclear envelope, providing evidence that Cx43 can participate in nucleocytoplasmic shuttling of small molecules. The accumulation of nuclear Cx43 during myogenic differentiation of cardiomyoblasts is suggested to modulate expression of genes implicated in this process. Altogether, our study provides new evidence for further defining the biological roles of nuclear Cx43, namely in cardiac pathophysiology.
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Affiliation(s)
- Tania Martins-Marques
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Katja Witschas
- Department of Basic Medical Sciences – Physiology group, Ghent University, 9000 Ghent, Belgium
| | - Ilda Ribeiro
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Cytogenetics and Genomics Laboratory (CIMAGO), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Mónica Zuzarte
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Steve Catarino
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Teresa Ribeiro-Rodrigues
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Francisco Caramelo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Trond Aasen
- Patologia Molecular Translacional, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
- CIBER de Cáncer (CIBERONC), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Isabel Marques Carreira
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Cytogenetics and Genomics Laboratory (CIMAGO), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Lino Goncalves
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Luc Leybaert
- Department of Basic Medical Sciences – Physiology group, Ghent University, 9000 Ghent, Belgium
| | - Henrique Girao
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
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7
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Chen YL, Xie XX, Zheng P, Zhu C, Ma H, Khalid Z, Xie YJ, Dang YZ, Ye Y, Sheng N, Zhong N, Lei WH, Zhang C, Zhang LJ, Jin T, Cao MJ. Selection, identification and crystal structure of shark-derived single-domain antibodies against a green fluorescent protein. Int J Biol Macromol 2023; 247:125852. [PMID: 37460076 DOI: 10.1016/j.ijbiomac.2023.125852] [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: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
Shark variable domain of new antigen receptors (VNARs) are the smallest naturally occurring binding domains with properties of low complexity, small size, cytoplasmic expression, and ease of engineering. Green fluorescent protein (GFP) molecules have been analyzed in conventional microscopy, but their spectral characteristics preclude their use in techniques offering substantially higher resolution. Besides, the GFP molecules can be quenched in acidic environment, which makes it necessary to develop anti-GFP antibody to solve these problems. In view of the diverse applications of GFP and unique physicochemical features of VNAR, the present study aims to generate VNARs against GFP. Here, we identified 36 VNARs targeting eCGP123, an extremely stable GFP, by phage display from three immunized sharks. These VNARs bound to eCGP123 with affinity constant KD values ranging from 6.76 to 605 nM. Among them, two lead VNARs named aGFP-14 and aGFP-15 with nanomolar eCGP123-binding affinity were selected for in-depth characterization. aGFP-14 and aGFP-15 recognized similar epitopes on eCGP123. X-ray crystallography studies clarified the mechanism by which aGFP14 interacts with eCGP123. aGFP-14 also showed cross-reaction with EGFP, with KD values of 47.2 nM. Finally, immunostaining analyses demonstrated that aGFP-14 was able to bind effectively to the EGFP expressed in both cultured cells and mouse brain tissues, and can be used as a fluorescence amplifier for EGFP. Our research demonstrates a feasible idea for the screening and production of shark-derived VNARs. The two high-affinity VNARs developed in the study contribute to the diversity of GFP sdAbs and may enhance the applications of GFP.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Peiyi Zheng
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Chenchen Zhu
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Huan Ma
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Zunera Khalid
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Yang-Jie Xie
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yi-Zhao Dang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Wen-Hui Lei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | | | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China.
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China.
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8
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Lee YB, Jung M, Kim J, Charles A, Christ W, Kang J, Kang MG, Kwak C, Klingström J, Smed-Sörensen A, Kim JS, Mun JY, Rhee HW. Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Rep 2023; 42:112835. [PMID: 37478010 DOI: 10.1016/j.celrep.2023.112835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a "plug-and-playable" PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Jiwoong Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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9
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of the autoinhibited SHIP1 inositol 5-phosphatase. J Biol Chem 2023; 299:105022. [PMID: 37423304 PMCID: PMC10448276 DOI: 10.1016/j.jbc.2023.105022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023] Open
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P3) lipids by PI3K. Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P3 to generate phosphatidylinositol-(3,4)-bisphosphate. Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single-molecule total internal reflection fluorescence microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that localization of the central catalytic domain of SHIP1 is insensitive to dynamic changes in PI(3,4,5)P3 and phosphatidylinositol-(3,4)-bisphosphate both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine and PI(3,4,5)P3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal Src homology 2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor-derived phosphopeptides presented either in solution or conjugated to a membrane. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid-binding specificity, protein-protein interactions, and the activation of autoinhibited SHIP1.
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Affiliation(s)
- Grace L Waddell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Emma E Drew
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Henry P Rupp
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Scott D Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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10
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Waddell GL, Drew EE, Rupp HP, Hansen SD. Mechanisms controlling membrane recruitment and activation of autoinhibited SHIP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.30.538895. [PMID: 37205499 PMCID: PMC10187190 DOI: 10.1101/2023.04.30.538895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P 3 ) lipids by phosphoinositide-3-kinase (PI3K). Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P 3 to generate PI(3,4)P 2 . Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single molecule TIRF microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that SHIP1's interactions with lipids are insensitive to dynamic changes in PI(3,4,5)P 3 both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine (PS) and PI(3,4,5)P 3 lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal SH2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor derived phosphopeptides presented either in solution or conjugated to supported membranes. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid binding specificity, protein-protein interactions, and activation of autoinhibited SHIP1.
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11
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A multifunctional peroxidase-based reaction for imaging, sensing and networking of spatial biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119428. [PMID: 36610614 DOI: 10.1016/j.bbamcr.2022.119428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
Peroxidase is a heme-containing enzyme that reduces hydrogen peroxide to water by extracting electron(s) from aromatic compounds via a sequential turnover reaction. This reaction can generate various aromatic radicals in the form of short-lived "spray" molecules. These can be either covalently attached to proximal proteins or polymerized via radical-radical coupling. Recent studies have shown that these peroxidase-generated radicals can be utilized as effective tools for spatial research in biological systems, including imaging studies aimed at the spatial localization of proteins using electron microscopy, spatial proteome mapping, and spatial sensing of metabolites (e.g., heme and hydrogen peroxide). This review may facilitate the wider utilization of these peroxidase-based methods for spatial discovery in cellular biology.
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12
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Tanner H, Sherwin O, Verkade P. Labelling strategies for correlative light electron microscopy. Microsc Res Tech 2023. [PMID: 36846978 DOI: 10.1002/jemt.24304] [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: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/01/2023]
Abstract
Imaging is one of the key technologies underpinning discoveries in biomedical research. Each imaging technique however usually only provides a specific type of information. For instance, live-cell imaging using fluorescent tags can show us the dynamics of a system. On the other hand, electron microscopy (EM) gives us better resolution combined with the structural reference space. By applying a combination of light and electron microscopy modalities to a single sample one can exploit the advantages of both techniques in correlative light electron microscopy (CLEM). Although CLEM approaches can generate additional insights into the sample that cannot be gained by either technique in isolation, the visualization of the object of interest via markers or probes is still one of the bottlenecks in a Correlative Microscopy workflow. Whereas fluorescence is not directly visible in a standard electron microscope, gold particles, as the most common choice of probe for EM can also only be visualized using specialized light microscopes. In this review we will discuss some of the latest developments of probes for CLEM and some strategies how to choose a probe, discussing pros and cons of specific probes, and ensuring that they function as a dual modality marker.
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Affiliation(s)
- Hugh Tanner
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK.,Department of Chemistry, KBC Building, Umeå University, Umeå, Sweden
| | - Olivia Sherwin
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Paul Verkade
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
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13
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Chen YL, Xie XX, Zhong N, Sun LC, Lin D, Zhang LJ, Weng L, Jin T, Cao MJ. Research Progresses and Applications of Fluorescent Protein Antibodies: A Review Focusing on Nanobodies. Int J Mol Sci 2023; 24:4307. [PMID: 36901737 PMCID: PMC10002328 DOI: 10.3390/ijms24054307] [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: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Since the discovery of fluorescent proteins (FPs), their rich fluorescence spectra and photochemical properties have promoted widespread biological research applications. FPs can be classified into green fluorescent protein (GFP) and its derivates, red fluorescent protein (RFP) and its derivates, and near-infrared FPs. With the continuous development of FPs, antibodies targeting FPs have emerged. The antibody, a class of immunoglobulin, is the main component of humoral immunity that explicitly recognizes and binds antigens. Monoclonal antibody, originating from a single B cell, has been widely applied in immunoassay, in vitro diagnostics, and drug development. The nanobody is a new type of antibody entirely composed of the variable domain of a heavy-chain antibody. Compared with conventional antibodies, these small and stable nanobodies can be expressed and functional in living cells. In addition, they can easily access grooves, seams, or hidden antigenic epitopes on the surface of the target. This review provides an overview of various FPs, the research progress of their antibodies, particularly nanobodies, and advanced applications of nanobodies targeting FPs. This review will be helpful for further research on nanobodies targeting FPs, making FPs more valuable in biological research.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Le-Chang Sun
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Duanquan Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
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14
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Sugar transporter Slc37a2 regulates bone metabolism in mice via a tubular lysosomal network in osteoclasts. Nat Commun 2023; 14:906. [PMID: 36810735 PMCID: PMC9945426 DOI: 10.1038/s41467-023-36484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Osteoclasts are giant bone-digesting cells that harbor specialized lysosome-related organelles termed secretory lysosomes (SLs). SLs store cathepsin K and serve as a membrane precursor to the ruffled border, the osteoclast's 'resorptive apparatus'. Yet, the molecular composition and spatiotemporal organization of SLs remains incompletely understood. Here, using organelle-resolution proteomics, we identify member a2 of the solute carrier 37 family (Slc37a2) as a SL sugar transporter. We demonstrate in mice that Slc37a2 localizes to the SL limiting membrane and that these organelles adopt a hitherto unnoticed but dynamic tubular network in living osteoclasts that is required for bone digestion. Accordingly, mice lacking Slc37a2 accrue high bone mass owing to uncoupled bone metabolism and disturbances in SL export of monosaccharide sugars, a prerequisite for SL delivery to the bone-lining osteoclast plasma membrane. Thus, Slc37a2 is a physiological component of the osteoclast's unique secretory organelle and a potential therapeutic target for metabolic bone diseases.
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15
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Kwon Y, Mehta S, Clark M, Walters G, Zhong Y, Lee HN, Sunahara RK, Zhang J. Non-canonical β-adrenergic activation of ERK at endosomes. Nature 2022; 611:173-179. [PMID: 36289326 PMCID: PMC10031817 DOI: 10.1038/s41586-022-05343-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
G-protein-coupled receptors (GPCRs), the largest family of signalling receptors, as well as important drug targets, are known to activate extracellular-signal-regulated kinase (ERK)-a master regulator of cell proliferation and survival1. However, the precise mechanisms that underlie GPCR-mediated ERK activation are not clearly understood2-4. Here we investigated how spatially organized β2-adrenergic receptor (β2AR) signalling controls ERK. Using subcellularly targeted ERK activity biosensors5, we show that β2AR signalling induces ERK activity at endosomes, but not at the plasma membrane. This pool of ERK activity depends on active, endosome-localized Gαs and requires ligand-stimulated β2AR endocytosis. We further identify an endosomally localized non-canonical signalling axis comprising Gαs, RAF and mitogen-activated protein kinase kinase, resulting in endosomal ERK activity that propagates into the nucleus. Selective inhibition of endosomal β2AR and Gαs signalling blunted nuclear ERK activity, MYC gene expression and cell proliferation. These results reveal a non-canonical mechanism for the spatial regulation of ERK through GPCR signalling and identify a functionally important endosomal signalling axis.
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Affiliation(s)
- Yonghoon Kwon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mary Clark
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Geneva Walters
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Yanghao Zhong
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Ha Neul Lee
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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17
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Agarwala S, Kim KY, Phan S, Ju S, Kong YE, Castillon GA, Bushong EA, Ellisman MH, Tamplin OJ. Defining the ultrastructure of the hematopoietic stem cell niche by correlative light and electron microscopy. eLife 2022; 11:64835. [PMID: 35943143 PMCID: PMC9391045 DOI: 10.7554/elife.64835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
The blood system is supported by hematopoietic stem and progenitor cells (HSPCs) found in a specialized microenvironment called the niche. Many different niche cell types support HSPCs, however how they interact and their ultrastructure has been difficult to define. Here, we show that single endogenous HSPCs can be tracked by light microscopy, then identified by serial block-face scanning electron microscopy (SBEM) at multiscale levels. Using the zebrafish larval kidney marrow (KM) niche as a model, we followed single fluorescently labeled HSPCs by light sheet microscopy, then confirmed their exact location in a 3D SBEM dataset. We found a variety of different configurations of HSPCs and surrounding niche cells, suggesting there could be functional heterogeneity in sites of HSPC lodgement. Our approach also allowed us to identify dopamine beta-hydroxylase (dbh) positive ganglion cells as a previously uncharacterized functional cell type in the HSPC niche. By integrating multiple imaging modalities, we could resolve the ultrastructure of single rare cells deep in live tissue and define all contacts between an HSPC and its surrounding niche cell types.
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Affiliation(s)
- Sobhika Agarwala
- Department of Pharmacology, University of Illinois at Chicago, Chicago, United States
| | - Keun-Young Kim
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Sebastien Phan
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Saeyeon Ju
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Ye Eun Kong
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Guillaume A Castillon
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Eric A Bushong
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, La Jolla, United States
| | - Owen J Tamplin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, United States
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18
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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19
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Ayuso-Jimeno IP, Ronchi P, Wang T, Gallori CE, Gross CT. Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy. Sci Rep 2022; 12:10213. [PMID: 35715545 PMCID: PMC9205864 DOI: 10.1038/s41598-022-14309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Enzymes that facilitate the local deposition of electron dense reaction products have been widely used as labels in electron microscopy (EM) for the identification of synaptic contacts in neural tissue. Peroxidases, in particular, can efficiently metabolize 3,3'-diaminobenzidine tetrahydrochloride hydrate (DAB) to produce precipitates with high contrast under EM following heavy metal staining, and can be genetically encoded to facilitate the labeling of specific cell-types or organelles. Nevertheless, the peroxidase/DAB method has so far not been reported to work in a multiplexed manner in combination with 3D volume EM techniques (e.g. Serial blockface electron microscopy, SBEM; Focused ion beam electron microscopy, FIBSEM) that are favored for the large-scale ultrastructural assessment of synaptic architecture However, a recently described peroxidase with enhanced enzymatic activity (dAPEX2) can efficienty deposit EM-visible DAB products in thick tissue without detergent treatment opening the possibility for the multiplex labeling of genetically defined cell-types in combination with volume EM methods. Here we demonstrate that multiplexed dAPEX2/DAB tagging is compatible with both FIBSEM and SBEM volume EM approaches and use them to map long-range genetically identified synaptic inputs from the anterior cingulate cortex to the periaqueductal gray in the mouse brain.
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Affiliation(s)
- Irene P Ayuso-Jimeno
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Paolo Ronchi
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory (EMBL), 69117, Meyerhofstr, Germany
| | - Tianzi Wang
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Catherine E Gallori
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy
| | - Cornelius T Gross
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Via Ramarini 32, 00015, Monterotondo, RM, Italy.
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20
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Hassing B, Candy A, Eaton CJ, Fernandes TR, Mesarich CH, Di Pietro A, Scott B. Localisation of phosphoinositides in the grass endophyte Epichloë festucae and genetic and functional analysis of key components of their biosynthetic pathway in E. festucae symbiosis and Fusarium oxysporum pathogenesis. Fungal Genet Biol 2022; 159:103669. [PMID: 35114379 DOI: 10.1016/j.fgb.2022.103669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022]
Abstract
Phosphoinositides (PI) are essential components of eukaryotic membranes and function in a large number of signaling processes. While lipid second messengers are well studied in mammals and yeast, their role in filamentous fungi is poorly understood. We used fluorescent PI-binding molecular probes to localize the phosphorylated phosphatidylinositol species PI[3]P, PI[3,5]P2, PI[4]P and PI[4,5]P2 in hyphae of the endophyte Epichloë festucae in axenic culture and during interaction with its grass host Lolium perenne. We also analysed the roles of the phosphatidylinositol-4-phosphate 5-kinase MssD and the predicted phosphatidylinositol-3,4,5-triphosphate 3-phosphatase TepA, a homolog of the mammalian tumour suppressor protein PTEN. Deletion of tepA in E. festucae and in the root-infecting tomato pathogen Fusarium oxysporum had no impact on growth in culture or the host interaction phenotype. However, this mutation did enable the detection of PI[3,4,5]P3 in septa and mycelium of E. festucae and showed that TepA is required for chemotropism in F. oxysporum. The identification of PI[3,4,5]P3 in ΔtepA strains suggests that filamentous fungi are able to generate PI[3,4,5]P3 and that fungal PTEN homologs are functional lipid phosphatases. The F. oxysporum chemotropism defect suggests a conserved role of PTEN homologs in chemotaxis across protists, fungi and mammals.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Alyesha Candy
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Carla J Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Tania R Fernandes
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Carl H Mesarich
- Bio-Protection Research Centre, New Zealand; School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand.
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21
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FACI Is a Novel CREB-H-Induced Protein That Inhibits Intestinal Lipid Absorption and Reverses Diet-Induced Obesity. Cell Mol Gastroenterol Hepatol 2022; 13:1365-1391. [PMID: 35093589 PMCID: PMC8938335 DOI: 10.1016/j.jcmgh.2022.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND & AIMS CREB-H is a key liver-enriched transcription factor governing lipid metabolism. Additional targets of CREB-H remain to be identified and characterized. Here, we identified a novel fasting- and CREB-H-induced (FACI) protein that inhibits intestinal lipid absorption and alleviates diet-induced obesity in mice. METHODS FACI was identified by reanalysis of existing transcriptomic data. Faci-/- mice were generated by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-mediated genome engineering. RNA sequencing was performed to identify differentially expressed genes in Faci-/- mice. Lipid accumulation in the villi was assessed by triglyceride measurement and Oil red O staining. In vitro fatty acid uptake assay was performed to verify in vivo findings. RESULTS FACI expression was enriched in liver and intestine. FACI is a phospholipid-binding protein that localizes to plasma membrane and recycling endosomes. Hepatic transcription of Faci was regulated by not only CREB-H, but also nutrient-responsive transcription factors sterol regulatory element-binding protein 1 (SREBP1), hepatocyte nuclear factor 4α (HNF4α), peroxisome proliferator-activated receptor γ coactivator-1α (PGC1α), and CREB, as well as fasting-related cyclic adenosine monophosphate (cAMP) signaling. Genetic knockout of Faci in mice showed an increase in intestinal fat absorption. In accordance with this, Faci deficiency aggravated high-fat diet-induced obesity, hyperlipidemia, steatosis, and other obesity-related metabolic dysfunction in mice. CONCLUSIONS FACI is a novel CREB-H-induced protein. Genetic disruption of Faci in mice showed its inhibitory effect on fat absorption and obesity. Our findings shed light on a new target of CREB-H implicated in lipid homeostasis.
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22
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Mishra PK, Kang MG, Lee H, Kim S, Choi S, Sharma N, Park CM, Ko J, Lee C, Seo JK, Rhee HW. A chemical tool for blue light-inducible proximity photo-crosslinking in live cells. Chem Sci 2022; 13:955-966. [PMID: 35211260 PMCID: PMC8790779 DOI: 10.1039/d1sc04871f] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
We developed a proximity photo-crosslinking method (Spotlight) with a 4-azido-N-ethyl-1,8-naphthalimide (AzNP) moiety that can be converted to reactive aryl nitrene species using ambient blue light-emitting diode light. Using an AzNP-conjugated HaloTag ligand (VL1), blue light-induced photo-crosslinked products of various HaloTag-conjugated proteins of interest were detected in subcellular spaces in live cells. Chemical or heat stress-induced dynamic changes in the proteome were also detected, and photo-crosslinking in the mouse brain tissue was enabled. Using Spotlight, we further identified the host interactome of SARS-CoV-2 nucleocapsid (N) protein, which is essential for viral genome assembly. Mass analysis of the VL1-crosslinked product of N-HaloTag in HEK293T cells showed that RNA-binding proteins in stress granules were exclusively enriched in the cross-linked samples. These results tell that our method can reveal the interactome of protein of interest within a short distance in live cells.
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Affiliation(s)
- Pratyush Kumar Mishra
- Department of Chemistry, Seoul National University Seoul 08826 Korea .,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44191 Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University Seoul 08826 Korea
| | - Hakbong Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Korea
| | - Seungjoon Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 Korea
| | - Subin Choi
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44191 Korea
| | - Nirmali Sharma
- Department of Chemistry, Seoul National University Seoul 08826 Korea .,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44191 Korea
| | - Cheol-Min Park
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44191 Korea
| | - Jaewon Ko
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST) Ulsan 44919 Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University Seoul 08826 Korea .,School of Biological Sciences, Seoul National University Seoul 08826 Korea
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23
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Kushner JS, Liu G, Eisert RJ, Bradshaw GA, Pitt GS, Hinson JT, Kalocsay M, Marx SO. Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics. Circ Res 2022; 130:273-287. [PMID: 35050691 PMCID: PMC8852690 DOI: 10.1161/circresaha.121.319810] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity purification and mass spectrometry, have revealed many macromolecular complexes in cardiomyocytes and the vasculature. Yet these methods often fail to identify in vivo or transient protein-protein interactions. To capture these interactions in living cells and animals with subsequent mass spectrometry identification, enzyme-catalyzed proximity labeling techniques have been developed in the past decade. Although the application of this methodology to cardiovascular research is still in its infancy, the field is developing rapidly, and the promise is substantial. In this review, we outline important concepts and discuss how proximity proteomics has been applied to study physiological and pathophysiological processes relevant to the cardiovascular system.
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Affiliation(s)
- Jared S. Kushner
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Guoxia Liu
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Robyn J. Eisert
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Gary A. Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Geoffrey S. Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College
| | - J. Travis Hinson
- Cardiology Center, UConn Health, Farmington, CT
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Marian Kalocsay
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Steven O. Marx
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
- Department of Molecular Pharmacology and Therapeutics, Columbia University, Vagelos College of Physicians and Surgeons
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24
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Groysbeck N, Donzeau M, Stoessel A, Haeberle AM, Ory S, Spehner D, Schultz P, Ersen O, Bahri M, Ihiawakrim D, Zuber G. Gold labelling of a green fluorescent protein (GFP)-tag inside cells using recombinant nanobodies conjugated to 2.4 nm thiolate-coated gold nanoparticles. NANOSCALE ADVANCES 2021; 3:6940-6948. [PMID: 36132366 PMCID: PMC9417625 DOI: 10.1039/d1na00256b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/24/2021] [Indexed: 06/15/2023]
Abstract
Advances in microscopy technology have prompted efforts to improve the reagents required to recognize specific molecules within the intracellular environment. For high-resolution electron microscopy, conjugation of selective binders originating from the immune response arsenal to gold nanoparticles (AuNPs) as contrasting agents is the method of choice to obtain labeling tools. However, conjugation of the minimal sized 15 kDa nanobody (Nb) to AuNPs remains challenging in comparison to the conjugation of 150 kDa IgG to AuNPs. Herein, effective Nb-AuNP assemblies are built using the selective and almost irreversible non-covalent associations between two peptide sequences deriving from a p53 heterotetramer domain variant. The 15 kDa GFP-binding Nb is fused to one dimerizing motif to obtain a recombinant Nb dimer with improved avidity for GFP while the other complementing dimerizing motif is equipped with thiols and grafted to a 2.4 nm substituted thiobenzoate-coordinated AuNP via thiolate exchange. After pegylation, the modified AuNPs are able to non-covalently anchor Nb dimers and the subsequent complexes demonstrate the ability to form immunogold label GFP-protein fusions within various subcellular locations. These tools open an avenue for precise localization of targets at high resolution by electron microscopy.
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Affiliation(s)
- Nadja Groysbeck
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Mariel Donzeau
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Audrey Stoessel
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Anne-Marie Haeberle
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives F-67000 Strasbourg France
| | - Stéphane Ory
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives F-67000 Strasbourg France
| | - Danièle Spehner
- Université de Strasbourg - Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire 67400 Illkirch France
| | - Patrick Schultz
- Université de Strasbourg - Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire 67400 Illkirch France
| | - Ovidiu Ersen
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Mounib Bahri
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Dris Ihiawakrim
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Guy Zuber
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
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25
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Lo HP, Lim YW, Xiong Z, Martel N, Ferguson C, Ariotti N, Giacomotto J, Rae J, Floetenmeyer M, Moradi SV, Gao Y, Tillu VA, Xia D, Wang H, Rahnama S, Nixon SJ, Bastiani M, Day RD, Smith KA, Palpant NJ, Johnston WA, Alexandrov K, Collins BM, Hall TE, Parton RG. Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle. J Cell Biol 2021; 220:e201905065. [PMID: 34633413 PMCID: PMC8513623 DOI: 10.1083/jcb.201905065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/02/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
The cavin proteins are essential for caveola biogenesis and function. Here, we identify a role for the muscle-specific component, Cavin4, in skeletal muscle T-tubule development by analyzing two vertebrate systems, mouse and zebrafish. In both models, Cavin4 localized to T-tubules, and loss of Cavin4 resulted in aberrant T-tubule maturation. In zebrafish, which possess duplicated cavin4 paralogs, Cavin4b was shown to directly interact with the T-tubule-associated BAR domain protein Bin1. Loss of both Cavin4a and Cavin4b caused aberrant accumulation of interconnected caveolae within the T-tubules, a fragmented T-tubule network enriched in Caveolin-3, and an impaired Ca2+ response upon mechanical stimulation. We propose a role for Cavin4 in remodeling the T-tubule membrane early in development by recycling caveolar components from the T-tubule to the sarcolemma. This generates a stable T-tubule domain lacking caveolae that is essential for T-tubule function.
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Affiliation(s)
- Harriet P. Lo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ye-Wheen Lim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Zherui Xiong
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick Martel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Charles Ferguson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jean Giacomotto
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service and University of Queensland, Brisbane, Queensland, Australia
| | - James Rae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthias Floetenmeyer
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Shayli Varasteh Moradi
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ya Gao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Vikas A. Tillu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, Brisbane, Queensland, Australia
| | - Huang Wang
- Translational Research Institute, Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Samira Rahnama
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Susan J. Nixon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Michele Bastiani
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ryan D. Day
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kelly A. Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nathan J. Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Wayne A. Johnston
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kirill Alexandrov
- CSIRO–Queensland University of Technology Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas E. Hall
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
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26
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Adhikari DP, Biener G, Stoneman MR, Badu DN, Paprocki JD, Eis A, Park PSH, Popa I, Raicu V. Comparative photophysical properties of some widely used fluorescent proteins under two-photon excitation conditions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120133. [PMID: 34243141 DOI: 10.1016/j.saa.2021.120133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Understanding the photophysical properties of fluorescent proteins (FPs), such as emission and absorption spectra, molecular brightness, photostability, and photo-switching, is critical to the development of criteria for their selection as tags for fluorescent-based biological applications. While two-photon excitation imaging techniques have steadily gained popularity - due to comparatively deeper penetration depth, reduced out-of-focus photobleaching, and wide separation between emission spectra and two-photon excitation spectra -, most studies reporting on the photophysical properties of FPs tend to remain focused on single-photon excitation. Here, we report our investigation of the photophysical properties of several commonly used fluorescent proteins using two-photon microscopy with spectral resolution in both excitation and emission. Our measurements indicate that not only the excitation (and sometimes emission) spectra of FPs may be markedly different between single-photon and two-photon excitation, but also their relative brightness and their photo-stability. A good understanding of the photophysical properties of FPs under two-photon excitation is essential for choosing the right tag(s) for a desired experiment.
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Affiliation(s)
- Dhruba P Adhikari
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Gabriel Biener
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | | | - Dammar N Badu
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Joel D Paprocki
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA
| | - Valerică Raicu
- Department of Physics, University of Wisconsin-Milwaukee, WI 53211, USA; Department of Biological Sciences, University of Wisconsin-Milwaukee, WI 53211, USA.
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27
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Williams AE, Shrivastava G, Gittis AG, Ganesan S, Martin-Martin I, Valenzuela Leon PC, Olson KE, Calvo E. Aedes aegypti Piwi4 Structural Features Are Necessary for RNA Binding and Nuclear Localization. Int J Mol Sci 2021; 22:ijms222312733. [PMID: 34884537 PMCID: PMC8657434 DOI: 10.3390/ijms222312733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway provides an RNA interference (RNAi) mechanism known from Drosophila studies to maintain the integrity of the germline genome by silencing transposable elements (TE). Aedes aegypti mosquitoes, which are the key vectors of several arthropod-borne viruses, exhibit an expanded repertoire of Piwi proteins involved in the piRNA pathway, suggesting functional divergence. Here, we investigate RNA-binding dynamics and subcellular localization of A. aegypti Piwi4 (AePiwi4), a Piwi protein involved in antiviral immunity and embryonic development, to better understand its function. We found that AePiwi4 PAZ (Piwi/Argonaute/Zwille), the domain that binds the 3′ ends of piRNAs, bound to mature (3′ 2′ O-methylated) and unmethylated RNAs with similar micromolar affinities (KD = 1.7 ± 0.8 μM and KD of 5.0 ± 2.2 μM, respectively; p = 0.05) in a sequence independent manner. Through site-directed mutagenesis studies, we identified highly conserved residues involved in RNA binding and found that subtle changes in the amino acids flanking the binding pocket across PAZ proteins have significant impacts on binding behaviors, likely by impacting the protein secondary structure. We also analyzed AePiwi4 subcellular localization in mosquito tissues. We found that the protein is both cytoplasmic and nuclear, and we identified an AePiwi4 nuclear localization signal (NLS) in the N-terminal region of the protein. Taken together, these studies provide insights on the dynamic role of AePiwi4 in RNAi and pave the way for future studies aimed at understanding Piwi interactions with diverse RNA populations.
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Affiliation(s)
- Adeline E. Williams
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Gaurav Shrivastava
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Apostolos G. Gittis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Sundar Ganesan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Paola Carolina Valenzuela Leon
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Ken E. Olson
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Correspondence: (K.E.O.); (E.C.)
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
- Correspondence: (K.E.O.); (E.C.)
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28
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Sepaniac LA, Martin W, Dionne LA, Stearns TM, Reinholdt LG, Stumpff J. Micronuclei in Kif18a mutant mice form stable micronuclear envelopes and do not promote tumorigenesis. J Cell Biol 2021; 220:212637. [PMID: 34515734 PMCID: PMC8441830 DOI: 10.1083/jcb.202101165] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/05/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
Micronuclei, whole or fragmented chromosomes spatially separated from the main nucleus, are associated with genomic instability and have been identified as drivers of tumorigenesis. Paradoxically, Kif18a mutant mice produce micronuclei due to asynchronous segregation of unaligned chromosomes in vivo but do not develop spontaneous tumors. We report here that micronuclei in Kif18a mutant mice form stable nuclear envelopes. Challenging Kif18a mutant mice via deletion of the Trp53 gene led to formation of thymic lymphoma with elevated levels of micronuclei. However, loss of Kif18a had modest or no effect on survival of Trp53 homozygotes and heterozygotes, respectively. Micronuclei in cultured KIF18A KO cells form stable nuclear envelopes characterized by increased recruitment of nuclear envelope components and successful expansion of decondensing chromatin compared with those induced by nocodazole washout or radiation. Lagging chromosomes were also positioned closer to the main chromatin masses in KIF18A KO cells. These data suggest that not all micronuclei actively promote tumorigenesis.
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Affiliation(s)
- Leslie A Sepaniac
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT
| | | | | | | | | | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT
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29
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Moreno-Layseca P, Jäntti NZ, Godbole R, Sommer C, Jacquemet G, Al-Akhrass H, Conway JRW, Kronqvist P, Kallionpää RE, Oliveira-Ferrer L, Cervero P, Linder S, Aepfelbacher M, Zauber H, Rae J, Parton RG, Disanza A, Scita G, Mayor S, Selbach M, Veltel S, Ivaska J. Cargo-specific recruitment in clathrin- and dynamin-independent endocytosis. Nat Cell Biol 2021; 23:1073-1084. [PMID: 34616024 DOI: 10.1038/s41556-021-00767-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
Spatially controlled, cargo-specific endocytosis is essential for development, tissue homeostasis and cancer invasion. Unlike cargo-specific clathrin-mediated endocytosis, the clathrin- and dynamin-independent endocytic pathway (CLIC-GEEC, CG pathway) is considered a bulk internalization route for the fluid phase, glycosylated membrane proteins and lipids. While the core molecular players of CG-endocytosis have been recently defined, evidence of cargo-specific adaptors or selective uptake of proteins for the pathway are lacking. Here we identify the actin-binding protein Swiprosin-1 (Swip1, EFHD2) as a cargo-specific adaptor for CG-endocytosis. Swip1 couples active Rab21-associated integrins with key components of the CG-endocytic machinery-Arf1, IRSp53 and actin-and is critical for integrin endocytosis. Through this function, Swip1 supports integrin-dependent cancer-cell migration and invasion, and is a negative prognostic marker in breast cancer. Our results demonstrate a previously unknown cargo selectivity for the CG pathway and a role for specific adaptors in recruitment into this endocytic route.
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Affiliation(s)
- Paulina Moreno-Layseca
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Niklas Z Jäntti
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rashmi Godbole
- National Centre for Biological Science (TIFR), Bangalore, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Christian Sommer
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Hussein Al-Akhrass
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Pauliina Kronqvist
- Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Roosa E Kallionpää
- Auria Biobank, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Pasquale Cervero
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Stefan Linder
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Henrik Zauber
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - James Rae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Andrea Disanza
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Satyajit Mayor
- National Centre for Biological Science (TIFR), Bangalore, India
| | - Matthias Selbach
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Stefan Veltel
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,Hochschule Bremen, City University of Applied Sciences, Bremen, Germany.
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. .,Department of Life Sciences, University of Turku, Turku, Finland. .,InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
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30
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Lyu X, Wang J, Wang J, Yin YS, Zhu Y, Li LL, Huang S, Peng S, Xue B, Liao R, Wang SQ, Long M, Wohland T, Chua BT, Sun Y, Li P, Chen XW, Xu L, Chen FJ, Li P. A gel-like condensation of Cidec generates lipid-permeable plates for lipid droplet fusion. Dev Cell 2021; 56:2592-2606.e7. [PMID: 34508658 DOI: 10.1016/j.devcel.2021.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 05/02/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Membrane contact between intracellular organelles is important in mediating organelle communication. However, the assembly of molecular machinery at membrane contact site and its internal organization correlating with its functional activity remain unclear. Here, we demonstrate that a gel-like condensation of Cidec, a crucial protein for obesity development by facilitating lipid droplet (LD) fusion, occurs at the LD-LD contact site (LDCS) through phase separation. The homomeric interaction between the multivalent N terminus of Cidec is sufficient to promote its phase separation both in vivo and in vitro. Interestingly, Cidec condensation at LDCSs generates highly plastic and lipid-permeable fusion plates that are geometrically constrained by donor LDs. In addition, Cidec condensates are distributed unevenly in the fusion plate generating stochastic sub-compartments that may represent unique lipid passageways during LD fusion. We have thus uncovered the organization and functional significance of geometry-constrained Cidec phase separation in mediating LD fusion and lipid homeostasis.
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Affiliation(s)
- Xuchao Lyu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianqin Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye-Sheng Yin
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yun Zhu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Lin-Lin Li
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Shuangru Huang
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Shuang Peng
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Boxin Xue
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Rongyu Liao
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi-Qiang Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Mian Long
- Institute of Mechanics, Chinese Academy of Sciences, No.15 Beisihuanxi Road, Beijing 100190, China
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Boon Tin Chua
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yujie Sun
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Center for Life Sciences and Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100101, China
| | - Li Xu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Feng-Jung Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
| | - Peng Li
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China.
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31
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Zhou Y, Ariotti N, Rae J, Liang H, Tillu V, Tee S, Bastiani M, Bademosi AT, Collins BM, Meunier FA, Hancock JF, Parton RG. Caveolin-1 and cavin1 act synergistically to generate a unique lipid environment in caveolae. J Cell Biol 2021; 220:211716. [PMID: 33496726 PMCID: PMC7844427 DOI: 10.1083/jcb.202005138] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Caveolae are specialized domains of the vertebrate cell surface with a well-defined morphology and crucial roles in cell migration and mechanoprotection. Unique compositions of proteins and lipids determine membrane architectures. The precise caveolar lipid profile and the roles of the major caveolar structural proteins, caveolins and cavins, in selectively sorting lipids have not been defined. Here, we used quantitative nanoscale lipid mapping together with molecular dynamic simulations to define the caveolar lipid profile. We show that caveolin-1 (CAV1) and cavin1 individually sort distinct plasma membrane lipids. Intact caveolar structures composed of both CAV1 and cavin1 further generate a unique lipid nano-environment. The caveolar lipid sorting capability includes selectivities for lipid headgroups and acyl chains. Because lipid headgroup metabolism and acyl chain remodeling are tightly regulated, this selective lipid sorting may allow caveolae to act as transit hubs to direct communications among lipid metabolism, vesicular trafficking, and signaling.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX
| | - Nicholas Ariotti
- University of New South Wales Sydney, Mark Wainwright Analytical Center, Sydney, New South Wales, Australia.,University of New South Wales Sydney, Department of Pathology, School of Medical Sciences, Kensington, Sydney, New South Wales, Australia
| | - James Rae
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX
| | - Vikas Tillu
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Shern Tee
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Michele Bastiani
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Adekunle T Bademosi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Brett M Collins
- University of New South Wales Sydney, Department of Pathology, School of Medical Sciences, Kensington, Sydney, New South Wales, Australia
| | - Frederic A Meunier
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Medical School, Houston, TX.,Program in Cell and Regulatory Biology, University of Texas Graduate School of Biomedical Sciences, Houston, TX
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland, Australia.,The University of Queensland, Centre for Microscopy and Microanalysis, Brisbane, Queensland, Australia
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32
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Bernard F, Jouette J, Durieu C, Le Borgne R, Guichet A, Claret S. GFP-Tagged Protein Detection by Electron Microscopy Using a GBP-APEX Tool in Drosophila. Front Cell Dev Biol 2021; 9:719582. [PMID: 34476234 PMCID: PMC8406855 DOI: 10.3389/fcell.2021.719582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022] Open
Abstract
In cell biology, detection of protein subcellular localizations is often achieved by optical microscopy techniques and more rarely by electron microscopy (EM) despite the greater resolution offered by EM. One of the possible reasons was that protein detection by EM required specific antibodies whereas this need could be circumvented by using fluorescently-tagged proteins in optical microscopy approaches. Recently, the description of a genetically encodable EM tag, the engineered ascorbate peroxidase (APEX), whose activity can be monitored by electron-dense DAB precipitates, has widened the possibilities of specific protein detection in EM. However, this technique still requires the generation of new molecular constructions. Thus, we decided to develop a versatile method that would take advantage of the numerous GFP-tagged proteins already existing and create a tool combining a nanobody anti-GFP (GBP) with APEX. This GBP-APEX tool allows a simple and efficient detection of any GFP fusion proteins without the needs of specific antibodies nor the generation of additional constructions. We have shown the feasibility and efficiency of this method to detect various proteins in Drosophila ovarian follicles such as nuclear proteins, proteins associated with endocytic vesicles, plasma membranes or nuclear envelopes. Lastly, we expressed this tool in Drosophila with the UAS/GAL4 system that enables spatiotemporal control of the protein detection.
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Affiliation(s)
- Fred Bernard
- Polarity and Morphogenesis Team, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
| | - Julie Jouette
- Polarity and Morphogenesis Team, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
| | - Catherine Durieu
- Imagoseine Platform, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
| | - Rémi Le Borgne
- Imagoseine Platform, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
| | - Antoine Guichet
- Polarity and Morphogenesis Team, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
| | - Sandra Claret
- Polarity and Morphogenesis Team, Institut Jacques Monod, CNRS, UMR 7592, University of Paris, Paris, France
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33
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Amiar S, Husby ML, Wijesinghe KJ, Angel S, Bhattarai N, Gerstman BS, Chapagain PP, Li S, Stahelin RV. Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. J Biol Chem 2021; 296:100796. [PMID: 34019871 PMCID: PMC8191294 DOI: 10.1016/j.jbc.2021.100796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 02/03/2023] Open
Abstract
Marburg virus (MARV) is a lipid-enveloped virus harboring a negative-sense RNA genome, which has caused sporadic outbreaks of viral hemorrhagic fever in sub-Saharan Africa. MARV assembles and buds from the host cell plasma membrane where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. The MARV matrix layer confers the virion filamentous shape and stability but how host lipids modulate mVP40 oligomerization is mostly unknown. Using in vitro and cellular techniques, we present a mVP40 assembly model highlighting two distinct oligomerization interfaces: the (N-terminal domain [NTD] and C-terminal domain [CTD]) in mVP40. Cellular studies of NTD and CTD oligomerization interface mutants demonstrate the importance of each interface in matrix assembly. The assembly steps include protein trafficking to the plasma membrane, homo-multimerization that induced protein enrichment, plasma membrane fluidity changes, and elongations at the plasma membrane. An ascorbate peroxidase derivative (APEX)-transmission electron microscopy method was employed to closely assess the ultrastructural localization and formation of viral particles for wildtype mVP40 and NTD and CTD oligomerization interface mutants. Taken together, these studies present a mechanistic model of mVP40 oligomerization and assembly at the plasma membrane during virion assembly that requires interactions with phosphatidylserine for NTD–NTD interactions and phosphatidylinositol-4,5-bisphosphate for proper CTD–CTD interactions. These findings have broader implications in understanding budding of lipid-enveloped viruses from the host cell plasma membrane and potential strategies to target protein–protein or lipid–protein interactions to inhibit virus budding.
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Affiliation(s)
- Souad Amiar
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Monica L Husby
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Kaveesha J Wijesinghe
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Stephanie Angel
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA.
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34
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Rae J, Ferguson C, Ariotti N, Webb RI, Cheng HH, Mead JL, Riches JD, Hunter DJ, Martel N, Baltos J, Christopoulos A, Bryce NS, Cagigas ML, Fonseka S, Sayre ME, Hardeman EC, Gunning PW, Gambin Y, Hall TE, Parton RG. A robust method for particulate detection of a genetic tag for 3D electron microscopy. eLife 2021; 10:64630. [PMID: 33904409 PMCID: PMC8104959 DOI: 10.7554/elife.64630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic tags allow rapid localization of tagged proteins in cells and tissues. APEX, an ascorbate peroxidase, has proven to be one of the most versatile and robust genetic tags for ultrastructural localization by electron microscopy (EM). Here, we describe a simple method, APEX-Gold, which converts the diffuse oxidized diaminobenzidine reaction product of APEX into a silver/gold particle akin to that used for immunogold labelling. The method increases the signal-to-noise ratio for EM detection, providing unambiguous detection of the tagged protein, and creates a readily quantifiable particulate signal. We demonstrate the wide applicability of this method for detection of membrane proteins, cytoplasmic proteins, and cytoskeletal proteins. The method can be combined with different EM techniques including fast freezing and freeze substitution, focussed ion beam scanning EM, and electron tomography. Quantitation of expressed APEX-fusion proteins is achievable using membrane vesicles generated by a cell-free expression system. These membrane vesicles possess a defined quantum of signal, which can act as an internal standard for determination of the absolute density of expressed APEX-fusion proteins. Detection of fusion proteins expressed at low levels in cells from CRISPR-edited mice demonstrates the high sensitivity of the APEX-Gold method.
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Affiliation(s)
- James Rae
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Charles Ferguson
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Nicholas Ariotti
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Richard I Webb
- The University of Queensland, Centre for Microscopy and Microanalysis, Queensland, Australia
| | - Han-Hao Cheng
- The University of Queensland, Centre for Microscopy and Microanalysis, Queensland, Australia
| | - James L Mead
- The University of Queensland, Centre for Microscopy and Microanalysis, Queensland, Australia.,Division Microrobotics and Control Engineering, Department of Computing Science, University of Oldenburg, Oldenburg, Germany
| | - James D Riches
- Queensland University of Technology, Queensland, Australia
| | - Dominic Jb Hunter
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia.,EMBL Australia Node for Single Molecule Sciences, University of New South Wales, Sydney, Australia
| | - Nick Martel
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Joanne Baltos
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Arthur Christopoulos
- Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Nicole S Bryce
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | | | - Sachini Fonseka
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Marcel E Sayre
- The University of Queensland, Centre for Microscopy and Microanalysis, Queensland, Australia
| | - Edna C Hardeman
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Peter W Gunning
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Sciences, University of New South Wales, Sydney, Australia
| | - Thomas E Hall
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia.,The University of Queensland, Centre for Microscopy and Microanalysis, Queensland, Australia
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35
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Xiong Z, Lo HP, McMahon KA, Martel N, Jones A, Hill MM, Parton RG, Hall TE. In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish. eLife 2021; 10:64631. [PMID: 33591275 PMCID: PMC7906605 DOI: 10.7554/elife.64631] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Protein interaction networks are crucial for complex cellular processes. However, the elucidation of protein interactions occurring within highly specialised cells and tissues is challenging. Here, we describe the development, and application, of a new method for proximity-dependent biotin labelling in whole zebrafish. Using a conditionally stabilised GFP-binding nanobody to target a biotin ligase to GFP-labelled proteins of interest, we show tissue-specific proteomic profiling using existing GFP-tagged transgenic zebrafish lines. We demonstrate the applicability of this approach, termed BLITZ (Biotin Labelling In Tagged Zebrafish), in diverse cell types such as neurons and vascular endothelial cells. We applied this methodology to identify interactors of caveolar coat protein, cavins, in skeletal muscle. Using this system, we defined specific interaction networks within in vivo muscle cells for the closely related but functionally distinct Cavin4 and Cavin1 proteins.
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Affiliation(s)
- Zherui Xiong
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Harriet P Lo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Kerrie-Ann McMahon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Nick Martel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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36
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Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation. Nat Commun 2021; 12:931. [PMID: 33568658 PMCID: PMC7875971 DOI: 10.1038/s41467-021-21035-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Caveolae are spherically shaped nanodomains of the plasma membrane, generated by cooperative assembly of caveolin and cavin proteins. Cavins are cytosolic peripheral membrane proteins with negatively charged intrinsically disordered regions that flank positively charged α-helical regions. Here, we show that the three disordered domains of Cavin1 are essential for caveola formation and dynamic trafficking of caveolae. Electrostatic interactions between disordered regions and α-helical regions promote liquid-liquid phase separation behaviour of Cavin1 in vitro, assembly of Cavin1 oligomers in solution, generation of membrane curvature, association with caveolin-1, and Cavin1 recruitment to caveolae in cells. Removal of the first disordered region causes irreversible gel formation in vitro and results in aberrant caveola trafficking through the endosomal system. We propose a model for caveola assembly whereby fuzzy electrostatic interactions between Cavin1 and caveolin-1 proteins, combined with membrane lipid interactions, are required to generate membrane curvature and a metastable caveola coat.
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37
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Zhang Z, Denans N, Liu Y, Zhulyn O, Rosenblatt HD, Wernig M, Barna M. Optogenetic manipulation of cellular communication using engineered myosin motors. Nat Cell Biol 2021; 23:198-208. [PMID: 33526902 PMCID: PMC7880895 DOI: 10.1038/s41556-020-00625-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022]
Abstract
Cells achieve highly efficient and accurate communication through cellular projections such as neurites and filopodia, yet there is a lack of genetically encoded tools that can selectively manipulate their composition and dynamics. Here, we present a versatile optogenetic toolbox of artificial multi-headed myosin motors that can move bidirectionally within long cellular extensions and allow for the selective transport of GFP-tagged cargo with light. Utilizing these engineered motors, we could transport bulky transmembrane receptors and organelles as well as actin remodellers to control the dynamics of both filopodia and neurites. Using an optimized in vivo imaging scheme, we further demonstrate that, upon limb amputation in axolotls, a complex array of filopodial extensions is formed. We selectively modulated these filopodial extensions and showed that they re-establish a Sonic Hedgehog signalling gradient during regeneration. Considering the ubiquitous existence of actin-based extensions, this toolbox shows the potential to manipulate cellular communication with unprecedented accuracy.
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Affiliation(s)
- Zijian Zhang
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nicolas Denans
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Yingfei Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Olena Zhulyn
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Hannah D Rosenblatt
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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38
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Xu D, Li P, Xu L. Characterization of the Role of Rab18 in Mediating LD-ER Contact and LD Growth. Methods Mol Biol 2021; 2293:229-241. [PMID: 34453721 DOI: 10.1007/978-1-0716-1346-7_16] [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] [Indexed: 01/13/2023]
Abstract
Lipid droplets (LDs) are dynamic cellular organelles found in most eukaryotic cells. Lipid incorporation from endoplasmic reticulum (ER) to LD is important in controlling LD growth and intracellular lipid homeostasis. However, the molecular link that mediates ER and LD cross talk remains elusive. Here, we describe the methodology used to characterize the function of Rab18 in regulating LD homeostasis and LD-ER contact. First, we focus on the quantitative assay used to measure intracellular LDs morphological changes. This is followed by a detailed description of the use of the APEX-label technology in combination with electron microscope (EM) to visualize ER-LD contact sites. These assays are valuable for the investigation of LD-associated proteins such as Rab18 in establishing membrane contact sites between LDs and other subcellular organelles.
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Affiliation(s)
- Dijin Xu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Li Xu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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39
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Parton RG, Kozlov MM, Ariotti N. Caveolae and lipid sorting: Shaping the cellular response to stress. J Cell Biol 2020; 219:133844. [PMID: 32328645 PMCID: PMC7147102 DOI: 10.1083/jcb.201905071] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/30/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Caveolae are an abundant and characteristic surface feature of many vertebrate cells. The uniform shape of caveolae is characterized by a bulb with consistent curvature connected to the plasma membrane (PM) by a neck region with opposing curvature. Caveolae act in mechanoprotection by flattening in response to increased membrane tension, and their disassembly influences the lipid organization of the PM. Here, we review evidence for caveolae as a specialized lipid domain and speculate on mechanisms that link changes in caveolar shape and/or protein composition to alterations in specific lipid species. We propose that high membrane curvature in specific regions of caveolae can enrich specific lipid species, with consequent changes in their localization upon caveolar flattening. In addition, we suggest how changes in the association of lipid-binding caveolar proteins upon flattening of caveolae could allow release of specific lipids into the bulk PM. We speculate that the caveolae-lipid system has evolved to function as a general stress-sensing and stress-protective membrane domain.
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Affiliation(s)
- Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Kensington, Australia.,Department of Pathology, School of Medical Sciences, The University of New South Wales, Kensington, Australia
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40
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Modular transient nanoclustering of activated β2-adrenergic receptors revealed by single-molecule tracking of conformation-specific nanobodies. Proc Natl Acad Sci U S A 2020; 117:30476-30487. [PMID: 33214152 DOI: 10.1073/pnas.2007443117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
None of the current superresolution microscopy techniques can reliably image the changes in endogenous protein nanoclustering dynamics associated with specific conformations in live cells. Single-domain nanobodies have been invaluable tools to isolate defined conformational states of proteins, and we reasoned that expressing these nanobodies coupled to single-molecule imaging-amenable tags could allow superresolution analysis of endogenous proteins in discrete conformational states. Here, we used anti-GFP nanobodies tagged with photoconvertible mEos expressed as intrabodies, as a proof-of-concept to perform single-particle tracking on a range of GFP proteins expressed in live cells, neurons, and small organisms. We next expressed highly specialized nanobodies that target conformation-specific endogenous β2-adrenoreceptor (β2-AR) in neurosecretory cells, unveiling real-time mobility behaviors of activated and inactivated endogenous conformers during agonist treatment in living cells. We showed that activated β2-AR (Nb80) is highly immobile and organized in nanoclusters. The Gαs-GPCR complex detected with Nb37 displayed higher mobility with surprisingly similar nanoclustering dynamics to that of Nb80. Activated conformers are highly sensitive to dynamin inhibition, suggesting selective targeting for endocytosis. Inactivated β2-AR (Nb60) molecules are also largely immobile but relatively less sensitive to endocytic blockade. Expression of single-domain nanobodies therefore provides a unique opportunity to capture highly transient changes in the dynamic nanoscale organization of endogenous proteins.
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41
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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42
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Ariotti N, Wu Y, Okano S, Gambin Y, Follett J, Rae J, Ferguson C, Teasdale RD, Alexandrov K, Meunier FA, Hill MM, Parton RG. An inverted CAV1 (caveolin 1) topology defines novel autophagy-dependent exosome secretion from prostate cancer cells. Autophagy 2020; 17:2200-2216. [DOI: 10.1080/15548627.2020.1820787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Nicholas Ariotti
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Mark Wainwright Analytical Centre, Electron Microscope Unit, The University of New South Wales, Sydney, Australia
| | - Yeping Wu
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Satomi Okano
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yann Gambin
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jordan Follett
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - James Rae
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Charles Ferguson
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Rohan D. Teasdale
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Kirill Alexandrov
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Frederic A. Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Michelle M. Hill
- UQ Diamantina Institute, The University of Queensland, Brisbane, Australia
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
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43
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Yang Z, Zhao X, Shang W, Liu Y, Ji JF, Liu JP, Tong C. Pyrroline-5-carboxylate synthase senses cellular stress and modulates metabolism by regulating mitochondrial respiration. Cell Death Differ 2020; 28:303-319. [PMID: 32770108 DOI: 10.1038/s41418-020-0601-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 11/09/2022] Open
Abstract
Pyrroline-5-carboxylate synthase (P5CS) catalyzes the synthesis of pyrroline-5-carboxylate (P5C), a key precursor for the synthesis of proline and ornithine. P5CS malfunction leads to multiple human diseases; however, the molecular mechanism underlying these diseases is unknown. We found that P5CS localizes in mitochondria in rod- and ring-like patterns but diffuses inside the mitochondria upon cellular starvation or exposure to oxidizing agents. Some of the human disease-related mutant forms of P5CS also exhibit diffused distribution. Multimerization (but not the catalytic activity) of P5CS regulates its localization. P5CS mutant cells have a reduced proliferation rate and are sensitive to cellular stresses. Flies lacking P5CS have reduced eclosion rates. Lipid droplets accumulate in the eyes of the newly eclosed P5CS mutant flies, which degenerate with aging. The loss of P5CS in cells leads to abnormal purine metabolism and lipid-droplet accumulation. The reduced lipid-droplet consumption is likely due to decreased expression of the fatty acid transporter, CPT1, and few β-oxidation-related genes following P5CS knockdown. Surprisingly, we found that P5CS is required for mitochondrial respiratory complex organization and that the respiration defects in P5CS knockout cells likely contribute to the metabolic defects in purine synthesis and lipid consumption. This study links amino acid synthesis with mitochondrial respiration and other key metabolic processes, whose imbalance might contribute to P5CS-related disease conditions.
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Affiliation(s)
- Zhaoying Yang
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaocui Zhao
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Weina Shang
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yang Liu
- Centre of Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jun-Feng Ji
- Centre of Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jun-Ping Liu
- Institute of Ageing Research, Hangzhou Normal University College of Medicine, Hangzhou, 311121, China
| | - Chao Tong
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,Institute of Ageing Research, Hangzhou Normal University College of Medicine, Hangzhou, 311121, China. .,The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
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44
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Du X, Zhou L, Aw YC, Mak HY, Xu Y, Rae J, Wang W, Zadoorian A, Hancock SE, Osborne B, Chen X, Wu JW, Turner N, Parton RG, Li P, Yang H. ORP5 localizes to ER-lipid droplet contacts and regulates the level of PI(4)P on lipid droplets. J Cell Biol 2020; 219:jcb.201905162. [PMID: 31653673 PMCID: PMC7039201 DOI: 10.1083/jcb.201905162] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/17/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022] Open
Abstract
Lipid droplets (LDs) are important organelles for cell metabolism. Here, Du et al. show that phosphatidylinositol-4-phosphate produced by PI4K2A can exist on LDs and is used/consumed by ORP5, which localizes to ER–LD contacts during the growth of LDs. Lipid droplets (LDs) are evolutionarily conserved organelles that play important roles in cellular metabolism. Each LD is enclosed by a monolayer of phospholipids, distinct from bilayer membranes. During LD biogenesis and growth, this monolayer of lipids expands by acquiring phospholipids from the endoplasmic reticulum (ER) through nonvesicular mechanisms. Here, in a mini-screen, we find that ORP5, an integral membrane protein of the ER, can localize to ER–LD contact sites upon oleate loading. ORP5 interacts with LDs through its ligand-binding domain, and ORP5 deficiency enhances neutral lipid synthesis and increases the size of LDs. Importantly, there is significantly more phosphatidylinositol-4-phosphate (PI(4)P) and less phosphatidylserine (PS) on LDs in ORP5-deficient cells than in normal cells. The increased presence of PI(4)P on LDs in ORP5-deficient cells requires phosphatidylinositol 4-kinase 2-α. Our results thus demonstrate the existence of PI(4)P on LDs and suggest that LD-associated PI(4)P may be primarily used by ORP5 to deliver PS to LDs.
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Affiliation(s)
- Ximing Du
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Linkang Zhou
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yvette Celine Aw
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Hoi Yin Mak
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Yanqing Xu
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - James Rae
- Centre for Microscopy and Microanalysis, Institute of Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Wenmin Wang
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Armella Zadoorian
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Sarah E Hancock
- School of Medical Sciences, The University of New South Wales, Sydney, Australia
| | - Brenna Osborne
- School of Medical Sciences, The University of New South Wales, Sydney, Australia
| | - Xiang Chen
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, China
| | - Jia-Wei Wu
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, China
| | - Nigel Turner
- School of Medical Sciences, The University of New South Wales, Sydney, Australia
| | - Robert G Parton
- Centre for Microscopy and Microanalysis, Institute of Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Peng Li
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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45
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Hall TE, Martel N, Ariotti N, Xiong Z, Lo HP, Ferguson C, Rae J, Lim YW, Parton RG. In vivo cell biological screening identifies an endocytic capture mechanism for T-tubule formation. Nat Commun 2020; 11:3711. [PMID: 32709891 PMCID: PMC7381618 DOI: 10.1038/s41467-020-17486-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
The skeletal muscle T-tubule is a specialized membrane domain essential for coordinated muscle contraction. However, in the absence of genetically tractable systems the mechanisms involved in T-tubule formation are unknown. Here, we use the optically transparent and genetically tractable zebrafish system to probe T-tubule development in vivo. By combining live imaging of transgenic markers with three-dimensional electron microscopy, we derive a four-dimensional quantitative model for T-tubule formation. To elucidate the mechanisms involved in T-tubule formation in vivo, we develop a quantitative screen for proteins that associate with and modulate early T-tubule formation, including an overexpression screen of the entire zebrafish Rab protein family. We propose an endocytic capture model involving firstly, formation of dynamic endocytic tubules at transient nucleation sites on the sarcolemma, secondly, stabilization by myofibrils/sarcoplasmic reticulum and finally, delivery of membrane from the recycling endosome and Golgi complex.
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Affiliation(s)
- Thomas E Hall
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Nick Martel
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Kensington, Australia
| | - Zherui Xiong
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Harriet P Lo
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Charles Ferguson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - James Rae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ye-Wheen Lim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia. .,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD, 4072, Australia.
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46
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Zhao M, Smith L, Volpatti J, Fabian L, Dowling JJ. Insights into wild-type dynamin 2 and the consequences of DNM2 mutations from transgenic zebrafish. Hum Mol Genet 2020; 28:4186-4196. [PMID: 31691805 DOI: 10.1093/hmg/ddz260] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/10/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022] Open
Abstract
Dynamin 2 (DNM2) encodes a ubiquitously expressed large GTPase with membrane fission capabilities that participates in the endocytosis of clathrin-coated vesicles. Heterozygous mutations in DNM2 are associated with two distinct neuromuscular disorders, Charcot-Marie-Tooth disease (CMT) and autosomal dominant centronuclear myopathy (CNM). Despite extensive investigations in cell culture, the role of dynamin 2 in normal muscle development is poorly understood and the consequences of DNM2 mutations at the molecular level in vivo are not known. To address these gaps in knowledge, we developed transgenic zebrafish expressing either wild-type dynamin 2 or dynamin 2 with either a CNM or CMT mutation. Taking advantage of the live imaging capabilities of the zebrafish embryo, we establish the localization of wild-type and mutant dynamin 2 in vivo, showing for the first time distinctive dynamin 2 subcellular compartments. Additionally, we demonstrate that CNM-related DNM2 mutations are associated with protein mislocalization and aggregation. Lastly, we define core phenotypes associated with our transgenic mutant fish, including impaired motor function and altered muscle ultrastructure, making them the ideal platform for drug screening. Overall, using the power of the zebrafish, we establish novel insights into dynamin 2 localization and dynamics and provide the necessary groundwork for future studies examining dynamin 2 pathomechanisms and therapy development.
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Affiliation(s)
- Mo Zhao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Lindsay Smith
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Jonathan Volpatti
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Lacramioara Fabian
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - James J Dowling
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Division of Neurology, The Hospital for Sick Children, Toronto, Canada.,Department of Pediatrics, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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47
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Serganova I, Blasberg RG. Molecular Imaging with Reporter Genes: Has Its Promise Been Delivered? J Nucl Med 2020; 60:1665-1681. [PMID: 31792128 DOI: 10.2967/jnumed.118.220004] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The first reporter systems were developed in the early 1980s and were based on measuring the activity of an enzyme-as a surrogate measure of promoter-driven transcriptional activity-which is now known as a reporter gene system. The initial objective and application of reporter techniques was to analyze the activity of a specific promoter (namely, the expression of a gene that is under the regulation of the specific promoter that is linked to the reporter gene). This system allows visualization of specific promoter activity with great sensitivity. In general, there are 2 classes of reporter systems: constitutively expressed (always-on) reporter constructs used for cell tracking, and inducible reporter systems sensitive to endogenous signaling molecules and transcription factors that characterize specific tissues, tumors, or signaling pathways.This review traces the development of different reporter systems, using fluorescent and bioluminescent proteins as well as radionuclide-based reporter systems. The development and application of radionuclide-based reporter systems is the focus of this review. The question at the end of the review is whether the "promise" of reporter gene imaging has been realized. What is required for moving forward with radionuclide-based reporter systems, and what is required for successful translation to clinical applications?
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Affiliation(s)
- Inna Serganova
- Department of Neurology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald G Blasberg
- Department of Neurology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York .,Department of Radiology, Memorial Hospital, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York; and.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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48
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Sultana S, Stewart J, van der Spoel AC. Truncated mutants of beta-glucosidase 2 (GBA2) are localized in the mitochondrial matrix and cause mitochondrial fragmentation. PLoS One 2020; 15:e0233856. [PMID: 32492073 PMCID: PMC7269613 DOI: 10.1371/journal.pone.0233856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
The enzyme β-glucosidase 2 (GBA2) is clinically relevant because it is targeted by the drug miglustat (Zavesca®) and because it is involved in inherited diseases. Mutations in the GBA2 gene are associated with two neurological diseases on the ataxia-spasticity spectrum, hereditary spastic paraplegia 46 (SPG46) and Marinesco-Sjögren-like syndrome (MSS). To establish how GBA2 mutations give rise to neurological pathology, we have begun to investigate mutant forms of GBA2 encoded by disease-associated GBA2 alleles. Previously, we found that five GBA2 missense mutants and five C-terminally truncated mutants lacked enzyme activity. Here we have examined the cellular locations of wild-type (WT) and mutant forms of GBA2 by confocal and electron microscopy, using transfected cells. Similar to GBA2-WT, the D594H and M510Vfs*17 GBA2 mutants were located at the plasma membrane, whereas the C-terminally truncated mutants terminating after amino acids 233 and 339 (GBA2-233 and -339) were present in the mitochondrial matrix, induced mitochondrial fragmentation and loss of mitochondrial transmembrane potential. Deletional mutagenesis indicated that residues 161–200 are critical for the mitochondrial fragmentation of GBA2-233 and -339. Considering that the mitochondrial fragmentation induced by GBA2-233 and -339 is consistently accompanied by their localization to the mitochondrial matrix, our deletional analysis raises the possibility that that GBA2 residues 161–200 harbor an internal targeting sequence for transport to the mitochondrial matrix. Altogether, our work provides new insights into the behaviour of GBA2-WT and disease-associated forms of GBA2.
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Affiliation(s)
- Saki Sultana
- The Atlantic Research Centre, Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jacklyn Stewart
- Biomedical Sciences Program, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Aarnoud C. van der Spoel
- The Atlantic Research Centre, Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- The Atlantic Research Centre, Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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49
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Ward KE, Sengupta R, Ropa JP, Amiar S, Stahelin RV. The Cytosolic Phospholipase A 2α N-terminal C2 Domain Binds and Oligomerizes on Membranes with Positive Curvature. Biomolecules 2020; 10:biom10040647. [PMID: 32331436 PMCID: PMC7226022 DOI: 10.3390/biom10040647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/04/2023] Open
Abstract
Group IV phospholipase A2α (cPLA2α) regulates the production of prostaglandins and leukotrienes via the formation of arachidonic acid from membrane phospholipids. The targeting and membrane binding of cPLA2α to the Golgi involves the N-terminal C2 domain, whereas the catalytic domain produces arachidonic acid. Although most studies of cPLA2α concern its catalytic activity, it is also linked to homeostatic processes involving the generation of vesicles that traffic material from the Golgi to the plasma membrane. Here we investigated how membrane curvature influences the homeostatic role of cPLA2α in vesicular trafficking. The cPLA2α C2 domain is known to induce changes in positive membrane curvature, a process which is dependent on cPLA2α membrane penetration. We showed that cPLA2α undergoes C2 domain-dependent oligomerization on membranes in vitro and in cells. We found that the association of the cPLA2α C2 domain with membranes is limited to membranes with positive curvature, and enhanced C2 domain oligomerization was observed on vesicles ~50 nm in diameter. We demonstrated that the cPLA2α C2 domain localizes to cholesterol enriched Golgi-derived vesicles independently of cPLA2α catalytic activity. Moreover, we demonstrate the C2 domain selectively localizes to lipid droplets whereas the full-length enzyme to a much lesser extent. Our results therefore provide novel insight into the molecular forces that mediate C2 domain-dependent membrane localization in vitro and in cells.
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Affiliation(s)
- Katherine E. Ward
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46556, USA; (K.E.W.); (J.P.R.)
| | - Ranjan Sengupta
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
| | - James P. Ropa
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46556, USA; (K.E.W.); (J.P.R.)
| | - Souad Amiar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +01-765-494-4152
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50
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Three-Dimensional Visualization of APEX2-Tagged Erg11 in Saccharomyces cerevisiae Using Focused Ion Beam Scanning Electron Microscopy. mSphere 2020; 5:5/1/e00981-19. [PMID: 32024705 PMCID: PMC7002314 DOI: 10.1128/msphere.00981-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The determination of the exact location of a protein in the cell is essential to the understanding of biological processes. Here, we report for the first time the visualization of a protein of interest in Saccharomyces cerevisiae using focused ion beam scanning electron microscopy (FIB-SEM). As a proof of concept, the integral endoplasmic reticulum (ER) membrane protein Erg11 has been C-terminally tagged with APEX2, which is an engineered peroxidase that catalyzes an electron-dense deposition of 3,3'-diaminobenzidine (DAB), as such marking the location of the fused protein of interest in electron microscopic images. As DAB is unable to cross the yeast cell wall to react with APEX2, cell walls have been partly removed by the formation of spheroplasts. This has resulted in a clear electron-dense ER signal for the Erg11 protein using FIB-SEM. With this study, we have validated the use of the APEX2 tag for visualization of yeast proteins in electron microscopy. Furthermore, we have introduced a methodology that enables precise and three-dimensional (3D) localization studies in yeast, with nanometer resolution and without the need for antibody staining. Because of these properties, the described technique can offer valuable information on the molecular functions of studied proteins.IMPORTANCE With this study, we have validated the use of the APEX2 tag to define the localization of proteins in the model yeast S. cerevisiae As such, FIB-SEM can identify the exact 3D location of a protein of interest in the cell with nanometer-scale resolution. Such detailed imaging could provide essential information on the elucidation of various biological processes. APEX2, which adds electron density to a fused protein of interest upon addition of the substrate DAB, originally was used in mammalian studies. With this study, we expand its use to protein localization studies in one of the most important models in molecular biology.
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