201
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Kang M, Lee J, Ko S, Shim SH. Prelabeling Expansion Single-Molecule Localization Microscopy with Minimal Linkage Error. Chembiochem 2021; 22:1396-1399. [PMID: 33325115 DOI: 10.1002/cbic.202000772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Indexed: 11/09/2022]
Abstract
Expansion microscopy combined with single-molecule localization microscopy (ExSMLM) has a potential for approaching molecular resolution. However, ExSMLM faces multiple challenges such as loss of fluorophores and proteins during polymerization, digestion or denaturation, and an increase in linkage error arising from the distance between the fluorophore and the target molecule. Here, we introduce a trifunctional streptavidin to link the target, fluorophore and gel matrix via a biotinylizable peptide tag. The resultant ExSMLM images of vimentin filaments demonstrated high labeling efficiency and a minimal linkage error of ∼5 nm. Our ExSMLM provides a simple and practical means for fluorescence imaging with molecular resolution.
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Affiliation(s)
- Minsu Kang
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Jooyong Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology(UNIST), Ulsan, 44919, Republic of Korea
| | - Sangyoon Ko
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Sang-Hee Shim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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202
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Van MV, Fujimori T, Bintu L. Nanobody-mediated control of gene expression and epigenetic memory. Nat Commun 2021; 12:537. [PMID: 33483487 PMCID: PMC7822885 DOI: 10.1038/s41467-020-20757-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
Targeting chromatin regulators to specific genomic locations for gene control is emerging as a powerful method in basic research and synthetic biology. However, many chromatin regulators are large, making them difficult to deliver and combine in mammalian cells. Here, we develop a strategy for gene control using small nanobodies that bind and recruit endogenous chromatin regulators to a gene. We show that an antiGFP nanobody can be used to simultaneously visualize GFP-tagged chromatin regulators and control gene expression, and that nanobodies against HP1 and DNMT1 can silence a reporter gene. Moreover, combining nanobodies together or with other regulators, such as DNMT3A or KRAB, can enhance silencing speed and epigenetic memory. Finally, we use the slow silencing speed and high memory of antiDNMT1 to build a signal duration timer and recorder. These results set the basis for using nanobodies against chromatin regulators for controlling gene expression and epigenetic memory.
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Affiliation(s)
- Mike V Van
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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203
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Eggers M, Rühl F, Haag F, Koch-Nolte F. Nanobodies as probes to investigate purinergic signaling. Biochem Pharmacol 2021; 187:114394. [PMID: 33388283 DOI: 10.1016/j.bcp.2020.114394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
Nanobodies (VHHs) are the single variable immunoglobulin domains of heavy chain antibodies (hcAbs) that naturally occur in alpacas and other camelids. The two variable domains of conventional antibodies typically interact via a hydrophobic interface. In contrast, the corresponding surface area of nanobodies is hydrophilic, rendering these single immunoglobulin domains highly soluble, robust to harsh environments, and exceptionally easy to format into bispecific reagents. In homage to Geoffrey Burnstock, the pioneer of purinergic signaling, we provide a brief history of nanobody-mediated modulation of purinergic signaling, using our nanobodies targeting P2X7 and the NAD+-metabolizing ecto-enzymes CD38 and ARTC2.2 as examples.
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Affiliation(s)
- Marie Eggers
- Institute of Immunology University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Felix Rühl
- Institute of Immunology University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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204
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OUP accepted manuscript. Microscopy (Oxf) 2021; 71:i72-i80. [DOI: 10.1093/jmicro/dfab048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/18/2021] [Accepted: 01/24/2022] [Indexed: 11/14/2022] Open
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205
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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206
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Nanobodies as Versatile Tool for Multiscale Imaging Modalities. Biomolecules 2020; 10:biom10121695. [PMID: 33353213 PMCID: PMC7767244 DOI: 10.3390/biom10121695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Molecular imaging is constantly growing in different areas of preclinical biomedical research. Several imaging methods have been developed and are continuously updated for both in vivo and in vitro applications, in order to increase the information about the structure, localization and function of molecules involved in physiology and disease. Along with these progresses, there is a continuous need for improving labeling strategies. In the last decades, the single domain antigen-binding fragments nanobodies (Nbs) emerged as important molecular imaging probes. Indeed, their small size (~15 kDa), high stability, affinity and modularity represent desirable features for imaging applications, providing higher tissue penetration, rapid targeting, increased spatial resolution and fast clearance. Accordingly, several Nb-based probes have been generated and applied to a variety of imaging modalities, ranging from in vivo and in vitro preclinical imaging to super-resolution microscopy. In this review, we will provide an overview of the state-of-the-art regarding the use of Nbs in several imaging modalities, underlining their extreme versatility and their enormous potential in targeting molecules and cells of interest in both preclinical and clinical studies.
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207
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Cui Y, Ma L, Schacke S, Yin JC, Hsueh YP, Jin H, Morrison H. Merlin cooperates with neurofibromin and Spred1 to suppress the Ras-Erk pathway. Hum Mol Genet 2020; 29:3793-3806. [PMID: 33331896 DOI: 10.1093/hmg/ddaa263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
The Ras-Erk pathway is frequently overactivated in human tumors. Neurofibromatosis types 1 and 2 (NF1, NF2) are characterized by multiple tumors of Schwann cell origin. The NF1 tumor suppressor neurofibromin is a principal Ras-GAP accelerating Ras inactivation, whereas the NF2 tumor suppressor merlin is a scaffold protein coordinating multiple signaling pathways. We have previously reported that merlin interacts with Ras and p120RasGAP. Here, we show that merlin can also interact with the neurofibromin/Spred1 complex via merlin-binding sites present on both proteins. Further, merlin can directly bind to the Ras-binding domain (RBD) and the kinase domain (KiD) of Raf1. As the third component of the neurofibromin/Spred1 complex, merlin cannot increase the Ras-GAP activity; rather, it blocks Ras binding to Raf1 by functioning as a 'selective Ras barrier'. Merlin-deficient Schwann cells require the Ras-Erk pathway activity for proliferation. Accordingly, suppression of the Ras-Erk pathway likely contributes to merlin's tumor suppressor activity. Taken together, our results, and studies by others, support targeting or co-targeting of this pathway as a therapy for NF2 inactivation-related tumors.
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Affiliation(s)
- Yan Cui
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Lin Ma
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Stephan Schacke
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Jiani C Yin
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310016, China
| | - Helen Morrison
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Germany
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208
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Perego E, Reshetniak S, Lorenz C, Hoffmann C, Milovanović D, Rizzoli SO, Köster S. A minimalist model to measure interactions between proteins and synaptic vesicles. Sci Rep 2020; 10:21086. [PMID: 33273508 PMCID: PMC7713060 DOI: 10.1038/s41598-020-77887-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/17/2020] [Indexed: 02/03/2023] Open
Abstract
Protein dynamics in the synaptic bouton are still not well understood, despite many quantitative studies of synaptic structure and function. The complexity of the synaptic environment makes investigations of presynaptic protein mobility challenging. Here, we present an in vitro approach to create a minimalist model of the synaptic environment by patterning synaptic vesicles (SVs) on glass coverslips. We employed fluorescence correlation spectroscopy (FCS) to measure the mobility of monomeric enhanced green fluorescent protein (mEGFP)-tagged proteins in the presence of the vesicle patterns. We observed that the mobility of all eleven measured proteins is strongly reduced in the presence of the SVs, suggesting that they all bind to the SVs. The mobility observed in these conditions is within the range of corresponding measurements in synapses of living cells. Overall, our simple, but robust, approach should enable numerous future studies of organelle-protein interactions in general.
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Affiliation(s)
- Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, 37077, Göttingen, Germany
| | - Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Charlotta Lorenz
- Institute for X-Ray Physics, University of Göttingen, 37077, Göttingen, Germany
| | - Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
| | - Dragomir Milovanović
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37075, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37073, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, 37077, Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37073, Göttingen, Germany.
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209
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A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nat Commun 2020; 11:6179. [PMID: 33268786 PMCID: PMC7710722 DOI: 10.1038/s41467-020-19884-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.
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210
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Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Dev Cell 2020; 56:111-124.e6. [PMID: 33238149 DOI: 10.1016/j.devcel.2020.10.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 02/02/2023]
Abstract
To date, the effects of specific modification types and sites on protein lifetime have not been systematically illustrated. Here, we describe a proteomic method, DeltaSILAC, to quantitatively assess the impact of site-specific phosphorylation on the turnover of thousands of proteins in live cells. Based on the accurate and reproducible mass spectrometry-based method, a pulse labeling approach using stable isotope-labeled amino acids in cells (pSILAC), phosphoproteomics, and a unique peptide-level matching strategy, our DeltaSILAC profiling revealed a global, unexpected delaying effect of many phosphosites on protein turnover. We further found that phosphorylated sites accelerating protein turnover are functionally selected for cell fitness, enriched in Cyclin-dependent kinase substrates, and evolutionarily conserved, whereas the glutamic acids surrounding phosphosites significantly delay protein turnover. Our method represents a generalizable approach and provides a rich resource for prioritizing the effects of phosphorylation sites on protein lifetime in the context of cell signaling and disease biology.
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Affiliation(s)
- Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qian Ba
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Dayun Lu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pingfu Hou
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Torsten Mueller
- German Cancer Research Center, DKFZ, 69120 Heidelberg, Germany
| | | | - Erli Gao
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yi Di
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
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211
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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212
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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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213
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Wierbowski BM, Petrov K, Aravena L, Gu G, Xu Y, Salic A. Hedgehog Pathway Activation Requires Coreceptor-Catalyzed, Lipid-Dependent Relay of the Sonic Hedgehog Ligand. Dev Cell 2020; 55:450-467.e8. [PMID: 33038332 DOI: 10.1016/j.devcel.2020.09.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/04/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022]
Abstract
Hedgehog signaling governs critical processes in embryogenesis, adult stem cell maintenance, and tumorigenesis. The activating ligand, Sonic hedgehog (SHH), is highly hydrophobic because of dual palmitate and cholesterol modification, and thus, its release from cells requires the secreted SCUBE proteins. We demonstrate that the soluble SCUBE-SHH complex, although highly potent in cellular assays, cannot directly signal through the SHH receptor, Patched1 (PTCH1). Rather, signaling by SCUBE-SHH requires a molecular relay mediated by the coreceptors CDON/BOC and GAS1, which relieves SHH inhibition by SCUBE. CDON/BOC bind both SCUBE and SHH, recruiting the complex to the cell surface. SHH is then handed off, in a dual lipid-dependent manner, to GAS1, and from GAS1 to PTCH1, initiating signaling. These results define an essential step in Hedgehog signaling, whereby coreceptors activate SHH by chaperoning it from a latent extracellular complex to its cell-surface receptor, and point to a broader paradigm of coreceptor function.
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Affiliation(s)
| | - Kostadin Petrov
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Aravena
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Garrick Gu
- Williams College, Williamstown, MA 01267, USA
| | - Yangqing Xu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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214
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Flicker S, Zettl I, Tillib SV. Nanobodies-Useful Tools for Allergy Treatment? Front Immunol 2020; 11:576255. [PMID: 33117377 PMCID: PMC7561424 DOI: 10.3389/fimmu.2020.576255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
In the last decade single domain antibodies (nanobodies, VHH) qualified through their unique characteristics have emerged as accepted and even advantageous alternative to conventional antibodies and have shown great potential as diagnostic and therapeutic tools. Currently nanobodies find their main medical application area in the fields of oncology and neurodegenerative diseases. According to late-breaking information, nanobodies specific for coronavirus spikes have been generated these days to test their suitability as useful therapeutics for future outbreaks. Their superior properties such as chemical stability, high affinity to a broad spectrum of epitopes, low immunogenicity, ease of their generation, selection and production proved nanobodies also to be remarkable to investigate their efficacy for passive treatment of type I allergy, an exaggerated immune reaction to foreign antigens with increasing global prevalence.
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Affiliation(s)
- Sabine Flicker
- Division of Immunopathology, Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ines Zettl
- Division of Immunopathology, Institute of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sergei V. Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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215
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Traenkle B, Segan S, Fagbadebo FO, Kaiser PD, Rothbauer U. A novel epitope tagging system to visualize and monitor antigens in live cells with chromobodies. Sci Rep 2020; 10:14267. [PMID: 32868807 PMCID: PMC7459311 DOI: 10.1038/s41598-020-71091-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Epitope tagging is a versatile approach to study different proteins using a well-defined and established methodology. To date, most epitope tags such as myc, HA, V5 and FLAG tags are recognized by antibodies, which limits their use to fixed cells, tissues or protein samples. Here we introduce a broadly applicable tagging strategy utilizing a short peptide tag (PepTag) which is specifically recognized by a nanobody (PepNB). We demonstrated that the PepNB can be easily functionalized for immunoprecipitation or direct immunofluorescence staining of Pep-tagged proteins in vitro. For in cellulo studies we converted the PepNB into a fluorescently labeled Pep-chromobody (PepCB) which is functionally expressed in living cells. The addition of the small PepTag does not interfere with the examined structures in different cellular compartments and its detection with the PepCB enables optical antigen tracing in real time. By employing the phenomenon of antigen-mediated chromobody stabilization (AMCBS) using a turnover-accelerated PepCB we demonstrated that the system is suitable to visualize and quantify changes in Pep-tagged antigen concentration by quantitative live-cell imaging. We expect that this novel tagging strategy offers new opportunities to study the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Sören Segan
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | | | - Philipp D Kaiser
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany. .,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany.
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216
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Muyldermans S. A guide to: generation and design of nanobodies. FEBS J 2020; 288:2084-2102. [PMID: 32780549 PMCID: PMC8048825 DOI: 10.1111/febs.15515] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/03/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
A nanobody (Nb) is a registered trademark of Ablynx, referring to the single antigen-binding domain of heavy chain-only antibodies (HCAbs) that are circulating in Camelidae. Nbs are produced recombinantly in micro-organisms and employed as research tools or for diagnostic and therapeutic applications. They were - and still are - also named single-domain antibodies (sdAbs) or variable domain of the heavy chain of HCAbs (VHH). A variety of methods are currently in use for the fast and efficient generation of target-specific Nbs. Such Nbs are produced at low cost and associate with high affinity to their cognate antigen. They are robust, strictly monomeric and easy to tailor into more complex entities to meet the requirements of their application. Here, we review the various sources and different strategies that have been developed to identify rapidly, target-specific Nbs. We further discuss a variety of engineering technologies that have been explored to broaden the application range of Nbs and summarise those applications where designed Nbs might offer a marked advantage over other affinity reagents.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Belgium.,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, China
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217
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Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae. PLoS Genet 2020; 16:e1008745. [PMID: 32845888 PMCID: PMC7478846 DOI: 10.1371/journal.pgen.1008745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/08/2020] [Accepted: 07/22/2020] [Indexed: 12/22/2022] Open
Abstract
Sphingolipids are abundant and essential molecules in eukaryotes that have crucial functions as signaling molecules and as membrane components. Sphingolipid biosynthesis starts in the endoplasmic reticulum with the condensation of serine and palmitoyl-CoA. Sphingolipid biosynthesis is highly regulated to maintain sphingolipid homeostasis. Even though, serine is an essential component of the sphingolipid biosynthesis pathway, its role in maintaining sphingolipid homeostasis has not been precisely studied. Here we show that serine uptake is an important factor for the regulation of sphingolipid biosynthesis in Saccharomyces cerevisiae. Using genetic experiments, we find the broad-specificity amino acid permease Gnp1 to be important for serine uptake. We confirm these results with serine uptake assays in gnp1Δ cells. We further show that uptake of exogenous serine by Gnp1 is important to maintain cellular serine levels and observe a specific connection between serine uptake and the first step of sphingolipid biosynthesis. Using mass spectrometry-based flux analysis, we further observed imported serine as the main source for de novo sphingolipid biosynthesis. Our results demonstrate that yeast cells preferentially use the uptake of exogenous serine to regulate sphingolipid biosynthesis. Our study can also be a starting point to analyze the role of serine uptake in mammalian sphingolipid metabolism. Sphingolipids (SPs) are membrane lipids globally required for eukaryotic life. In contrast to other lipid classes, SPs cannot be stored in the cell and therefore their levels have to be tightly regulated. Failure to maintain sphingolipid homeostasis can result in pathologies including neurodegeneration, childhood asthma and cancer. However, we are only starting to understand how SP biosynthesis is adjusted according to need. In this study, we use genetic and biochemical methods to show that the uptake of exogenous serine is necessary to maintain SP homeostasis in Saccharomyces cerevisiae. Serine is one of the precursors of long chain bases in cells, the first intermediate of SP metabolism. Our results suggest that the uptake of serine is directly coupled to SP biosynthesis at ER-plasma membrane contact sites. Overall, our study identifies serine uptake as a novel regulatory factor of SP homeostasis. While we use yeast as a discovery tool, these results also provide valuable insights into mammalian SP biology especially under pathological conditions.
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218
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Sillen M, Weeks SD, Strelkov SV, Declerck PJ. Structural Insights into the Mechanism of a Nanobody That Stabilizes PAI-1 and Modulates Its Activity. Int J Mol Sci 2020; 21:ijms21165859. [PMID: 32824134 PMCID: PMC7461574 DOI: 10.3390/ijms21165859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1) is the main physiological inhibitor of tissue-type (tPA) and urokinase-type (uPA) plasminogen activators (PAs). Apart from being critically involved in fibrinolysis and wound healing, emerging evidence indicates that PAI-1 plays an important role in many diseases, including cardiovascular disease, tissue fibrosis, and cancer. Targeting PAI-1 is therefore a promising therapeutic strategy in PAI-1 related pathologies. Despite ongoing efforts no PAI-1 inhibitors were approved to date for therapeutic use in humans. A better understanding of the molecular mechanisms of PAI-1 inhibition is therefore necessary to guide the rational design of PAI-1 modulators. Here, we present a 1.9 Å crystal structure of PAI-1 in complex with an inhibitory nanobody VHH-s-a93 (Nb93). Structural analysis in combination with biochemical characterization reveals that Nb93 directly interferes with PAI-1/PA complex formation and stabilizes the active conformation of the PAI-1 molecule.
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Affiliation(s)
- Machteld Sillen
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium;
| | - Stephen D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium; (S.D.W); (S.V.S.)
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium; (S.D.W); (S.V.S.)
| | - Paul J. Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium;
- Correspondence:
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219
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Ren J, Zhang C, Ji F, Jia L. Characterization and comparison of two peptide-tag specific nanobodies for immunoaffinity chromatography. J Chromatogr A 2020; 1624:461227. [PMID: 32540069 DOI: 10.1016/j.chroma.2020.461227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Affinity chromatography is generally regarded as a powerful tool allowing the single step purification of recombinant proteins with high purity and yields. However, for most protein products, affinity purification methods for industrial applications are not readily available, mainly due to the lack of specific and robust natural counterparts that could function as affinity ligands. In this study, we explored the applicability of nanobody-based peptide-tag immunorecognition systems as a platform for affinity chromatography. Two typical nanobodies (BC2-nb and Syn2-nb) that are capable of recognizing specifically a particular peptide-tag, were prepared through prokaryotic expression and proved to be able to bind with nanomolar affinity to their cognate tag fused to enhanced green fluorescent protein (eGFP). Through an epoxy-based immobilization reaction, the two nanobodies were coupled on a Sepharose CL-6B matrix under the same conditions. The remaining antigen binding activity of the immobilized BC2-nb and Syn2-nb was determined to be 83.1% and 42.9%, yielding the resins with the dynamic binding capacity (DBC) of 21.4 mg/mL and 5.9 mg/mL, respectively. The immobilized affinity ligands exhibited high binding specificity towards their respective target peptides, yielding a product purity above 90% directly from crude bacterial lysates in one single chromatographic step. However, for the both affinity complexes, desorption has been found difficult, and effective recovery of the bound products could be only achieved with competitive elution or after employing harsh conditions such as 10 mM NaOH solution, which will compromise the reuse cycles of the affinity resins. This study shows the potential of nanobody-based affinity chromatography for efficient purification of recombinant proteins especially from complex feedstocks and reveals the primary issues to be addressed to develop a successful application.
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Affiliation(s)
- Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116023, PR China.
| | - Chao Zhang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116023, PR China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116023, PR China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116023, PR China.
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220
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Poc P, Gutzeit VA, Ast J, Lee J, Jones BJ, D'Este E, Mathes B, Lehmann M, Hodson DJ, Levitz J, Broichhagen J. Interrogating surface versus intracellular transmembrane receptor populations using cell-impermeable SNAP-tag substrates. Chem Sci 2020; 11:7871-7883. [PMID: 34123074 PMCID: PMC8163392 DOI: 10.1039/d0sc02794d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/02/2020] [Indexed: 01/13/2023] Open
Abstract
Employing self-labelling protein tags for the attachment of fluorescent dyes has become a routine and powerful technique in optical microscopy to visualize and track fused proteins. However, membrane permeability of the dyes and the associated background signals can interfere with the analysis of extracellular labelling sites. Here we describe a novel approach to improve extracellular labelling by functionalizing the SNAP-tag substrate benzyl guanine ("BG") with a charged sulfonate ("SBG"). This chemical manipulation can be applied to any SNAP-tag substrate, improves solubility, reduces non-specific staining and renders the bioconjugation handle impermeable while leaving its cargo untouched. We report SBG-conjugated fluorophores across the visible spectrum, which cleanly label SNAP-fused proteins in the plasma membrane of living cells. We demonstrate the utility of SBG-conjugated fluorophores to interrogate class A, B and C G protein-coupled receptors (GPCRs) using a range of imaging approaches including nanoscopic superresolution imaging, analysis of GPCR trafficking from intra- and extracellular pools, in vivo labelling in mouse brain and analysis of receptor stoichiometry using single molecule pull down.
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Affiliation(s)
- Pascal Poc
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Medicine New York NY 10065 USA
| | - Julia Ast
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
| | - Ben J Jones
- Section of Investigative Medicine, Imperial College London London W12 0NN UK
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research Heidelberg Germany
| | - Bettina Mathes
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Pharmacology and Cell Biology Robert-Rössle-Str. 10 13125 Berlin Germany
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology New York NY 10065 USA
| | - Johannes Broichhagen
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Chemical Biology Robert-Rössle-Str. 10 13125 Berlin Germany
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221
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Hansen JN, Kaiser F, Klausen C, Stüven B, Chong R, Bönigk W, Mick DU, Möglich A, Jurisch-Yaksi N, Schmidt FI, Wachten D. Nanobody-directed targeting of optogenetic tools to study signaling in the primary cilium. eLife 2020; 9:e57907. [PMID: 32579112 PMCID: PMC7338050 DOI: 10.7554/elife.57907] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Compartmentalization of cellular signaling forms the molecular basis of cellular behavior. The primary cilium constitutes a subcellular compartment that orchestrates signal transduction independent from the cell body. Ciliary dysfunction causes severe diseases, termed ciliopathies. Analyzing ciliary signaling has been challenging due to the lack of tools to investigate ciliary signaling. Here, we describe a nanobody-based targeting approach for optogenetic tools in mammalian cells and in vivo in zebrafish to specifically analyze ciliary signaling and function. Thereby, we overcome the loss of protein function observed after fusion to ciliary targeting sequences. We functionally localized modifiers of cAMP signaling, the photo-activated adenylyl cyclase bPAC and the light-activated phosphodiesterase LAPD, and the cAMP biosensor mlCNBD-FRET to the cilium. Using this approach, we studied the contribution of spatial cAMP signaling in controlling cilia length. Combining optogenetics with nanobody-based targeting will pave the way to the molecular understanding of ciliary function in health and disease.
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Affiliation(s)
- Jan N Hansen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Fabian Kaiser
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Christina Klausen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Birthe Stüven
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Raymond Chong
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
| | - Wolfgang Bönigk
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar)BonnGermany
| | - David U Mick
- Center for Molecular Signaling (PZMS), Center of Human and Molecular Biology (ZHMB), Saarland University, School of MedicineHomburgGermany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Universität BayreuthBayreuthGermany
- Research Center for Bio-Macromolecules, Universität BayreuthBayreuthGermany
- Bayreuth Center for Biochemistry & Molecular Biology, Universität BayreuthBayreuthGermany
| | - Nathalie Jurisch-Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, The Faculty of Medicine, Norwegian University of Science and TechnologyTrondheimNorway
- Department of Neurology and Clinical Neurophysiology, St. Olavs University HospitalTrondheimNorway
| | - Florian I Schmidt
- Institute of Innate Immunity, Emmy Noether research group, Medical Faculty, University of BonnBonnGermany
- Core Facility Nanobodies, University of BonnBonnGermany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of BonnBonnGermany
- Research Group Molecular Physiology, Center of Advanced European Studies and Research (caesar)BonnGermany
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222
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Gerdes C, Waal N, Offner T, Fornasiero EF, Wender N, Verbarg H, Manzini I, Trenkwalder C, Mollenhauer B, Strohäker T, Zweckstetter M, Becker S, Rizzoli SO, Basmanav FB, Opazo F. A nanobody-based fluorescent reporter reveals human α-synuclein in the cell cytosol. Nat Commun 2020; 11:2729. [PMID: 32483166 PMCID: PMC7264335 DOI: 10.1038/s41467-020-16575-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Aggregation and spreading of α-Synuclein (αSyn) are hallmarks of several neurodegenerative diseases, thus monitoring human αSyn (hαSyn) in animal models or cell cultures is vital for the field. However, the detection of native hαSyn in such systems is challenging. We show that the nanobody NbSyn87, previously-described to bind hαSyn, also shows cross-reactivity for the proteasomal subunit Rpn10. As such, when the NbSyn87 is expressed in the absence of hαSyn, it is continuously degraded by the proteasome, while it is stabilized when it binds to hαSyn. Here, we exploit this feature to design a new Fluorescent Reporter for hαSyn (FluoReSyn) by fusing NbSyn87 to fluorescent proteins, which results in fluorescence signal fluctuations depending on the presence and amounts of intracellular hαSyn. We characterize this biosensor in cells and tissues to finally reveal the presence of transmittable αSyn in human cerebrospinal fluid, demonstrating the potential of FluoReSyn for clinical research and diagnostics.
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Affiliation(s)
- Christoph Gerdes
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Natalia Waal
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Thomas Offner
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus-Liebig University Giessen, 35390, Giessen, Germany
- Institute of Neurophysiology and Cellular Biophysics, University of Göttingen, Göttingen, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Nora Wender
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Hannes Verbarg
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Ivan Manzini
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus-Liebig University Giessen, 35390, Giessen, Germany
- Institute of Neurophysiology and Cellular Biophysics, University of Göttingen, Göttingen, Germany
| | - Claudia Trenkwalder
- Department of Neurosurgery, University Medical Center Göttingen, D-37075, Göttingen, Germany
- Paracelsus-Elena-Klinik, Klinikstraße 16, 34128, Kassel, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Klinikstraße 16, 34128, Kassel, Germany
- Department of Neurology, University Medical Center Göttingen, D-37075, Göttingen, Germany
| | - Timo Strohäker
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Göttingen, Germany
| | - Fitnat Buket Basmanav
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
- Campus Laboratory for Advanced Imaging, Microscopy and Spectroscopy, University of Göttingen, D-37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37073, Göttingen, Germany.
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223
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de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020; 172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Antibody fragments for which the sequence is available are suitable for straightforward engineering and expression in both eukaryotic and prokaryotic systems. When produced as fusions with convenient tags, they become reagents which pair their selective binding capacity to an orthogonal function. Several kinds of immunoreagents composed by nanobodies and either large proteins or short sequences have been designed for providing inexpensive ready-to-use biological tools. The possibility to choose among alternative expression strategies is critical because the fusion moieties might require specific conditions for correct folding or post-translational modifications. In the case of nanobody production, the trend is towards simpler but reliable (bacterial) methods that can substitute for more cumbersome processes requiring the use of eukaryotic systems. The use of these will not disappear, but will be restricted to those cases in which the final immunoconstructs must have features that cannot be obtained in prokaryotic cells. At the same time, bacterial expression has evolved from the conventional procedure which considered exclusively the nanobody and nanobody-fusion accumulation in the periplasm. Several reports show the advantage of cytoplasmic expression, surface-display and secretion for at least some applications. Finally, there is an increasing interest to use as a model the short nanobody sequence for the development of in silico methodologies aimed at optimizing the yields, stability and affinity of recombinant antibodies. There is an increasing request for immunoreagents based on nanobodies. The multiplicity of their applications requires constructs with different structural complexity. Alternative expression methods are necessary to achieve such structural requirements. In silico optimization of nanobody biophysical characteristics becomes more and more reliable.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, S-5000, Nova Gorica, Slovenia.
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224
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Cialek CA, Koch AL, Galindo G, Stasevich TJ. Lighting up single-mRNA translation dynamics in living cells. Curr Opin Genet Dev 2020; 61:75-82. [PMID: 32408104 PMCID: PMC7508770 DOI: 10.1016/j.gde.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/12/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022]
Abstract
Over the past five years, technological advances have made it possible to image the translation of single mRNA in the natural context of living cells. With these advances, researchers are beginning to shed light on when, where, and to what degree mRNA are translated with single-molecule precision. These works provide insight into the heterogeneity of translation amongst single transcripts, behavior that is averaged out in complementary bulk assays. In this review, we discuss the rapidly maturing field of live-cell, single-mRNA imaging of translation, beginning with a brief overview of recent technological advances. The remainder of the review focuses on the new biological insights gained from these technologies. We conclude with a discussion of the future of this technology.
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Affiliation(s)
- Charlotte A Cialek
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 2268503, Japan.
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225
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Affiliation(s)
- Alexander M Marzilli
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Jeffrey B McMahan
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - John T Ngo
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA.
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226
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Farrants H, Tarnawski M, Müller TG, Otsuka S, Hiblot J, Koch B, Kueblbeck M, Kräusslich HG, Ellenberg J, Johnsson K. Chemogenetic Control of Nanobodies. Nat Methods 2020; 17:279-282. [PMID: 32066961 DOI: 10.1038/s41592-020-0746-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/01/2019] [Accepted: 01/15/2020] [Indexed: 12/30/2022]
Abstract
We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.
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Affiliation(s)
- Helen Farrants
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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