1
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Zhu FY, Mei LJ, Tian R, Li C, Wang YL, Xiang SL, Zhu MQ, Tang BZ. Recent advances in super-resolution optical imaging based on aggregation-induced emission. Chem Soc Rev 2024; 53:3350-3383. [PMID: 38406832 DOI: 10.1039/d3cs00698k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.
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Affiliation(s)
- Feng-Yu Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Li-Jun Mei
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Rui Tian
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Chong Li
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Ya-Long Wang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Shi-Li Xiang
- Hubei Jiufengshan Laboratory, Wuhan, 430206, China
| | - Ming-Qiang Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China.
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2
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Hoang MN, Peterbauer C. Double-Labeling Method for Visualization and Quantification of Membrane-Associated Proteins in Lactococcus lactis. Int J Mol Sci 2023; 24:10586. [PMID: 37445764 DOI: 10.3390/ijms241310586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Lactococcus lactis displaying recombinant proteins on its surface can be used as a potential drug delivery vector in prophylactic medication and therapeutic treatments for many diseases. These applications enable live-cell mucosal and oral administration, providing painless, needle-free solutions and triggering robust immune response at the site of pathogen entry. Immunization requires quantitative control of antigens and, ideally, a complete understanding of the bacterial processing mechanism applied to the target proteins. In this study, we propose a double-labeling method based on a conjugated dye specific for a recombinantly introduced polyhistidine tag (to visualize surface-exposed proteins) and a membrane-permeable dye specific for a tetra-cysteine tag (to visualize cytoplasmic proteins), combined with a method to block the labeling of surface-exposed tetra-cysteine tags, to clearly obtain location-specific signals of the two dyes. This allows simultaneous detection and quantification of targeted proteins on the cell surface and in the cytoplasm. Using this method, we were able to detect full-length peptide chains for the model proteins HtrA and BmpA in L. lactis, which are associated with the cell membrane by two different attachment modes, and thus confirm that membrane-associated proteins in L. lactis are secreted using the Sec-dependent post-translational pathway. We were able to quantitatively follow cytoplasmic protein production and accumulation and subsequent export and surface attachment, which provides a convenient tool for monitoring these processes for cell surface display applications.
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Affiliation(s)
- Mai Ngoc Hoang
- Institute of Immunology, Department of Human Medicine, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany
| | - Clemens Peterbauer
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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3
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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4
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Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021; 86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
Abstract
Nearly all proteins are synthesized in the cytosol. The majority of this proteome must be trafficked elsewhere, such as to membranes, to subcellular compartments, or outside of the cell. Proper trafficking of nascent protein is necessary for protein folding, maturation, quality control and cellular and organismal health. To better understand cellular biology, molecular and chemical technologies to properly characterize protein trafficking (and mistrafficking) have been developed and applied. Herein, we take a biochemical perspective to review technologies that enable spatial and temporal measurement of protein distribution, focusing on both the most widely adopted methodologies and exciting emerging approaches.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
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5
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Wolf S, Wan Y, McDole K. Current approaches to fate mapping and lineage tracing using image data. Development 2021; 148:dev198994. [PMID: 34498046 DOI: 10.1242/dev.198994] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visualizing, tracking and reconstructing cell lineages in developing embryos has been an ongoing effort for well over a century. Recent advances in light microscopy, labelling strategies and computational methods to analyse complex image datasets have enabled detailed investigations into the fates of cells. Combined with powerful new advances in genomics and single-cell transcriptomics, the field of developmental biology is able to describe the formation of the embryo like never before. In this Review, we discuss some of the different strategies and applications to lineage tracing in live-imaging data and outline software methodologies that can be applied to various cell-tracking challenges.
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Affiliation(s)
- Steffen Wolf
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yinan Wan
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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6
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Vong K, Tahara T, Urano S, Nasibullin I, Tsubokura K, Nakao Y, Kurbangalieva A, Onoe H, Watanabe Y, Tanaka K. Disrupting tumor onset and growth via selective cell tagging (SeCT) therapy. SCIENCE ADVANCES 2021; 7:7/17/eabg4038. [PMID: 33893089 PMCID: PMC8064634 DOI: 10.1126/sciadv.abg4038] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/08/2021] [Indexed: 05/16/2023]
Abstract
This study presents the early framework of selective cell tagging (SeCT) therapy, which is the concept of preferentially labeling specific cells in vivo with chemical moieties that can elicit a therapeutic response. Using glycosylated artificial metalloenzyme (GArM)-based protein labeling, this study reports two separate functional strategies. In one approach, early tumor onset can be suppressed by tagging cancer cells in living mice with an integrin-blocking cyclic-Arg-Gly-Asp (cRGD) moiety, thereby disrupting cell adhesion onto the extracellular matrix. In another approach, tumor growth in mice can be reduced by tagging with a cytotoxic doxorubicin moiety. Subsequent cell death occurs following internalization and drug release. Overall, experiments have shown that mouse populations receiving the mixture of SeCT labeling reagents exhibited a significant delay/reduction in tumor onset and growth compared with controls. Highlighting its adaptability, this work represents a foundational step for further development of SeCT therapy and its potential therapeutic applications.
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Affiliation(s)
- Kenward Vong
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Tsuyoshi Tahara
- RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Sayaka Urano
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Igor Nasibullin
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Kazuki Tsubokura
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- School of Advanced Science and Engineering, Department of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoichi Nakao
- School of Advanced Science and Engineering, Department of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Almira Kurbangalieva
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
| | - Hirotaka Onoe
- RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Katsunori Tanaka
- Biofunctional Synthetic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
- GlycoTargeting Research Laboratory, RIKEN Baton Zone Program, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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8
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Laxman P, Ansari S, Gaus K, Goyette J. The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy. Front Chem 2021; 9:641355. [PMID: 33842432 PMCID: PMC8027105 DOI: 10.3389/fchem.2021.641355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. An upcoming field of protein labeling is incorporating unnatural amino acids (UAAs) with an attached fluorescent dye for precise localization and visualization of individual molecules. For this technique, fluorescent probes are conjugated to UAAs and are introduced into the protein of interest (POI) as a label. Here we contrast this labeling method with other commonly used protein-based labeling methods such as fluorescent proteins (FPs) or self-labeling tags such as Halotag, SNAP-tags, and CLIP-tags, and highlight the benefits and shortcomings of the site-specific incorporation of UAAs coupled with fluorescent dyes in SMLM.
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Affiliation(s)
| | | | | | - Jesse Goyette
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Sciences, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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9
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Adler S, Motiei L, Mankovski N, Cohen H, Margulies D. Fluorescent Labelling of Cell Surface Proteins on a Solid Support. Isr J Chem 2021. [DOI: 10.1002/ijch.202100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sean Adler
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Leila Motiei
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Naama Mankovski
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Hagai Cohen
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - David Margulies
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
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10
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Vaghela R, Arkudas A, Horch RE, Hessenauer M. Actually Seeing What Is Going on - Intravital Microscopy in Tissue Engineering. Front Bioeng Biotechnol 2021; 9:627462. [PMID: 33681162 PMCID: PMC7925911 DOI: 10.3389/fbioe.2021.627462] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Intravital microscopy (IVM) study approach offers several advantages over in vitro, ex vivo, and 3D models. IVM provides real-time imaging of cellular events, which provides us a comprehensive picture of dynamic processes. Rapid improvement in microscopy techniques has permitted deep tissue imaging at a higher resolution. Advances in fluorescence tagging methods enable tracking of specific cell types. Moreover, IVM can serve as an important tool to study different stages of tissue regeneration processes. Furthermore, the compatibility of different tissue engineered constructs can be analyzed. IVM is also a promising approach to investigate host reactions on implanted biomaterials. IVM can provide instant feedback for improvising tissue engineering strategies. In this review, we aim to provide an overview of the requirements and applications of different IVM approaches. First, we will discuss the history of IVM development, and then we will provide an overview of available optical modalities including the pros and cons. Later, we will summarize different fluorescence labeling methods. In the final section, we will discuss well-established chronic and acute IVM models for different organs.
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Affiliation(s)
- Ravikumar Vaghela
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas Arkudas
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Raymund E Horch
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Maximilian Hessenauer
- Department of Plastic and Hand Surgery, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
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11
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 269] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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12
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Sueda S. Enzyme-based protein-tagging systems for site-specific labeling of proteins in living cells. ACTA ACUST UNITED AC 2020; 69:156-166. [PMID: 32166307 DOI: 10.1093/jmicro/dfaa011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 11/13/2022]
Abstract
Various protein-labeling methods based on the specific interactions between genetically encoded tags and synthetic probes have been proposed to complement fluorescent protein-based labeling. In particular, labeling methods based on enzyme reactions have been intensively developed by taking advantage of the highly specific interactions between enzymes and their substrates. In this approach, the peptides or proteins are genetically attached to the target proteins as a tag, and the various labels are then incorporated into the tags by enzyme reactions with the substrates carrying those labels. On the other hand, we have been developing an enzyme-based protein-labeling system distinct from the existing ones. In our system, the substrate protein is attached to the target proteins as a tag, and the labels are incorporated into the tag by post-translational modification with an enzyme carrying those labels followed by tight complexation between the enzyme and the substrate protein. In this review, I summarize the enzyme-based protein-labeling systems with a focus on several typical methods and then describe our labeling system based on tight complexation between the enzyme and the substrate protein.
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Affiliation(s)
- Shinji Sueda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8502, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu 804-8550, Japan
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13
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Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020. [PMID: 32235926 DOI: 10.1038/s41596-020-0313-319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
When used appropriately, a confocal fluorescence microscope is an excellent tool for making quantitative measurements in cells and tissues. The confocal microscope's ability to block out-of-focus light and thereby perform optical sectioning through a specimen allows the researcher to quantify fluorescence with very high spatial precision. However, generating meaningful data using confocal microscopy requires careful planning and a thorough understanding of the technique. In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments. Common pitfalls such as photobleaching and cross-talk are addressed, as well as several troubling instrumentation problems that may prevent the acquisition of quantitative data. Finally, guidelines for analyzing and presenting confocal images in a way that maintains the quantitative nature of the data are presented, and statistical analysis is discussed. A visual summary of this tutorial is available as a poster (https://doi.org/10.1038/s41596-020-0307-7).
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Affiliation(s)
- James Jonkman
- Advanced Optical Microscopy Facility (AOMF), University Health Network, Toronto, Ontario, Canada.
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Graham D Wright
- A*STAR Microscopy Platform (AMP), Skin Research Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kurt I Anderson
- Crick Advanced Light Microscopy Facility (CALM), The Francis Crick Institute, London, UK
| | - Alison J North
- Bio-Imaging Resource Center, The Rockefeller University, New York, NY, USA
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14
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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15
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Jonkman J, Brown CM, Wright GD, Anderson KI, North AJ. Tutorial: guidance for quantitative confocal microscopy. Nat Protoc 2020; 15:1585-1611. [DOI: 10.1038/s41596-020-0313-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 02/10/2020] [Indexed: 01/04/2023]
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16
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Zhang L, Kang J, Liu S, Zhang X, Sun J, Hu Y, Yang Y, Chen L. A chemical covalent tactic for bio-thiol sensing and protein labeling agent design. Chem Commun (Camb) 2020; 56:11485-11488. [DOI: 10.1039/d0cc04169f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A chemical covalent tactic was developed for bio-thiol sensing and protein labeling agent design by the installation of a sulfoxide scaffold onto the skeleton of various fluorophores.
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Affiliation(s)
- Liangwei Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Jie Kang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Shudi Liu
- College of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Xia Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Jinyu Sun
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yuesong Hu
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yang Yang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
- China
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17
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Gao MY, Chen Q, Li W, Shen AG, Hu JM. Combined Surface-Enhanced Raman Scattering Emissions for High-Throughput Optical Labels on Micrometer-Scale Objects. Anal Chem 2019; 91:13866-13873. [DOI: 10.1021/acs.analchem.9b03357] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meng-Yue Gao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Qiao Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Wei Li
- Hubei Key Laboratory of Biomass Fiber and Eco-dyeing & Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan 430073, People’s Republic of China
| | - Ai-Guo Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Ji-Ming Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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18
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MacNevin CJ, Watanabe T, Weitzman M, Gulyani A, Fuehrer S, Pinkin NK, Tian X, Liu F, Jin J, Hahn KM. Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells. J Am Chem Soc 2019; 141:7275-7282. [PMID: 30994345 DOI: 10.1021/jacs.8b09841] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dyes with environment-sensitive fluorescence have proven useful to study the spatiotemporal dynamics of protein activity in living cells. When attached to proteins, their fluorescence can reflect protein conformational changes, post-translational modifications, or protein interactions. However, the utility of such dye-protein conjugates has been limited because it is difficult to load them into cells. They usually must be introduced using techniques that perturb cell physiology, limit throughput, or generate fluorescent vesicles (e.g., electroporation, microinjection, or membrane transduction peptides). Here we circumvent these problems by modifying a proven, environment-sensitive biosensor fluorophore so that it can pass through cell membranes without staining intracellular compartments and can be attached to proteins within living cells using unnatural amino acid (UAA) mutagenesis. Reactive groups were incorporated for attachment to UAAs or small molecules (mero166, azide; mero167, alkyne; mero76, carboxylic acid). These dyes are bright and fluoresce at long wavelengths (reaching ε = 100 000 M-1 cm-1, ϕ = 0.24, with excitation 565 nm and emission 594 nm). The utility of mero166 was demonstrated by in-cell labeling of a UAA to generate a biosensor for the small GTPase Cdc42. In addition, conjugation of mero166 to a small molecule produced a membrane-permeable probe that reported the localization of the DNA methyltransferase G9a in cells. This approach provides a strategy to access biosensors for many targets and to more practically harness the varied environmental sensitivities of synthetic dyes.
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Affiliation(s)
- Christopher J MacNevin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew Weitzman
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Akash Gulyani
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sheryl Fuehrer
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nicholas K Pinkin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Xu Tian
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Klaus M Hahn
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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19
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Bauer C, Duwald R, Labrador GM, Pascal S, Moneva Lorente P, Bosson J, Lacour J, Rochaix JD. Specific labeling of mitochondria of Chlamydomonas with cationic helicene fluorophores. Org Biomol Chem 2019; 16:919-923. [PMID: 29334105 DOI: 10.1039/c7ob02906c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Twelve cationic helicenes and one triangulene were tested for the specific labeling of mitochondria from algal cells. Octyl ester derivative 5 readily penetrates algal cells and gives rise to clear fluorescence patterns when it is used at concentrations in the μM range. Under these conditions, cell structures are well preserved and cell survival is not compromised. Cationic helicene compounds such as 5 provide new useful tools for examining the mitochondrial network and its dynamics including fission and fusion events.
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Affiliation(s)
- Christoph Bauer
- Bioimaging Center, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
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20
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 532] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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21
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Bisseret P, Abdelkafi H, Blanchard N. Aryl transition metal chemical warheads for protein bioconjugation. Chem Sci 2018; 9:5132-5144. [PMID: 29997865 PMCID: PMC6001634 DOI: 10.1039/c8sc00780b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/22/2018] [Indexed: 12/16/2022] Open
Abstract
The past seven years have witnessed the burgeoning of protein bioconjugation reactions highlighting aryl transition metal reagents as coupling partners. This new bioorthogonal organometallic chemistry, which sets the scene for stoichiometric processes in place of the catalytic procedures that developed in parallel, already enabled the forging of C-S and C-C bonds onto protein substrates, respectively in their native state or equipped with pre-installed non-natural terminal alkene or alkyne appendages. Although not yet applied to proteins, related transformations pointing to the creation of C-N bonds have, in addition, just been disclosed by targeting peptide lysine residues. Central to this research was the selection of ligands attached to the transition metal, in order to confer to metal complexes, not only their stability in aqueous medium, but also the desired chemoselectivity. We summarize here this body of work, which has already put in the limelight elaborated palladium and gold complexes equipped with biologically relevant appendages, such as fluorescent and affinity tags, as well as drug molecules. This research holds much promise, not only for the study of proteins themselves, but also for the design of new protein-based biotherapeutics, such as protein-drug conjugates or constrained analogs resulting from macrocyclisation reactions.
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Affiliation(s)
- Philippe Bisseret
- Université de Haute-Alsace , Université de Strasbourg , CNRS , LIMA , UMR 7042 , 68000 Mulhouse , France . https://bsm.unistra.fr ; ;
| | - Hajer Abdelkafi
- Université de Haute-Alsace , Université de Strasbourg , CNRS , LIMA , UMR 7042 , 68000 Mulhouse , France . https://bsm.unistra.fr ; ;
| | - Nicolas Blanchard
- Université de Haute-Alsace , Université de Strasbourg , CNRS , LIMA , UMR 7042 , 68000 Mulhouse , France . https://bsm.unistra.fr ; ;
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22
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Cao J, Ge R, Zhang M, Xia J, Han S, Lu W, Liang Y, Zhang T, Sun Y. A triple modality BSA-coated dendritic nanoplatform for NIR imaging, enhanced tumor penetration and anticancer therapy. NANOSCALE 2018; 10:9021-9037. [PMID: 29717725 DOI: 10.1039/c7nr09552j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Functional theranostic systems for drug delivery capable of concurrent near-infrared (NIR) fluorescence imaging, active tumor targeting and anticancer therapies are desired for concise cancer diagnosis and treatment. Dendrimers with controllable size and surface functionalities are good candidates for such platforms. However, integration of active targeting ligands and imaging agents separately on the surface or encapsulation of the imaging agents in the inner core of the dendrimers will result in a more complex composition or reduced drug loading efficiency. Herein, we reported a PAMAM-based theranostic system, with a simple integrin-specific imaging ligand prepared from two motifs. One motif is a NIR carbocyanine fluorescent dye (Cyp) for precise in vivo monitoring of the system and identification of tumor or cancer cells, and the other is a novel tumor-penetrating cyclic peptide (CRGDKGPDC, abbreviated iRGD). BSA was non-covalently bonded with Cyp to reduce NIR agent fluorescence-quenching aggregates and enhance imaging signals. The chemotherapy effect of these dendritic systems was achieved by encapsulating paclitaxel into the hydrophobic interior of the dendrimers. In vitro and in vivo targeting and penetrating studies revealed that a significantly high amount of the dendritic systems was endocytosed by HepG2 cells and enhanced accumulation and penetration at tumor sites. Our safety evaluation showed that masking of cationic-end groups of PAMAM to neutral or anionic groups has resulted in decreased or even zero-toxicity. The preliminary antitumor efficacy of the dendritic system was evaluated. In vitro and in vivo studies confirmed that paclitaxel-encapsulated functionalized PAMAM can efficiently kill HepG2 cancer cells. In conclusion, our functionalized theranostic dendritic system could be a promising nanocarrier to effectively deliver drugs to deep tumor regions for anticancer therapy.
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Affiliation(s)
- Jie Cao
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China.
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23
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Xu S, Hu HY. Fluorogen-activating proteins: beyond classical fluorescent proteins. Acta Pharm Sin B 2018; 8:339-348. [PMID: 29881673 PMCID: PMC5989828 DOI: 10.1016/j.apsb.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/11/2018] [Accepted: 02/18/2018] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs)/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems.
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Affiliation(s)
- Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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24
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Noe F, Frey T, Fiedler J, Geithe C, Nowak B, Krautwurst D. IL-6-HaloTag ® enables live-cell plasma membrane staining, flow cytometry, functional expression, and de-orphaning of recombinant odorant receptors. J Biol Methods 2017; 4:e81. [PMID: 31453235 PMCID: PMC6706138 DOI: 10.14440/jbm.2017.206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022] Open
Abstract
The assignment of cognate odorant/agonist pairs is a prerequisite for an understanding of odorant coding at the receptor level. However, the identification of new ligands for odorant receptors (ORs) in cell-based assays has been challenging, due to their individual and rather sub-optimal plasma membrane expression, as compared with other G protein-coupled receptors. Accessory proteins, such as the chaperone RTP1S, or Ric8b, have improved the surface expression of at least a portion of ORs. Typically, recombinant ORs carry N-terminal tags, which proved helpful for their functional membrane expression. The most common tag is the 'Rho-tag', representing an N-terminal part of rhodopsin, but also 'Lucy-' or 'Flag-tag' extensions have been described. Here, we used a bi-functional N-terminal tag, called 'interleukin 6 (IL-6)-HaloTag®', with IL-6 facilitating functional cell surface expression of recombinant ORs, and the HaloTag® protein, serving as a highly specific acceptor for cell-impermeant or cell-permeant, fluorophore-coupled ligands, which enable the quantification of odorant receptor expression by live-cell flow cytometry. Our experiments revealed on average an about four-fold increased surface expression, a four-fold higher signaling amplitude, and a significantly higher potency of odorant-induced cAMP signaling of six different human IL-6-HaloTag®-ORs across five different receptor families in NxG 108CC15 cells, as compared to their Rho-tag-HaloTag® constructs. We observed similar results in HEK-293 cells. Moreover, screening an IL-6-HaloTag®-odorant receptor library with allyl phenyl acetate, revealed both known receptors as best responders for this compound. In summary, the IL-6-HaloTag® represents a promising tool for the de-orphaning of ORs.
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Affiliation(s)
| | | | | | | | | | - Dietmar Krautwurst
- Deutsche Forschungsanstalt für Lebensmittelchemie – Leibniz Institut, D-85354 Freising, Germany
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25
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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26
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Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE. Super-Resolution Microscopy and Single-Protein Tracking in Live Bacteria Using a Genetically Encoded, Photostable Fluoromodule. ACTA ACUST UNITED AC 2017. [PMID: 28627757 DOI: 10.1002/cpcb.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types. However, their use in bacteria has been limited due to challenges imposed by a complex bacterial cell wall. Here, we describe the use of a genetically encoded photostable fluoromodule that can be targeted to cytosolic and membrane proteins in the Gram negative bacterium Caulobacter crescentus. Additionally, we summarize methods to use this fluoromodule for single protein imaging and super-resolution microscopy using stimulated emission depletion. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, California
| | - Adam M Perez
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California.,Department of Biology, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucy Shapiro
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California
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27
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Wallisch M, Sulmann S, Koch KW, Christoffers J. Bifunctional Diaminoterephthalate Fluorescent Dye as Probe for Cross-Linking Proteins. Chemistry 2017; 23:6535-6543. [DOI: 10.1002/chem.201700774] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Melanie Wallisch
- Institut für Chemie; Carl von Ossietzky-Universität Oldenburg; 26111 Oldenburg Germany
| | - Stefan Sulmann
- Biochemistry Group, Department of Neuroscience; Carl von Ossietzky-Universität Oldenburg; 26111 Oldenburg Germany
| | - Karl-Wilhelm Koch
- Biochemistry Group, Department of Neuroscience; Carl von Ossietzky-Universität Oldenburg; 26111 Oldenburg Germany
| | - Jens Christoffers
- Institut für Chemie; Carl von Ossietzky-Universität Oldenburg; 26111 Oldenburg Germany
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28
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Farrants H, Hiblot J, Griss R, Johnsson K. Rational Design and Applications of Semisynthetic Modular Biosensors: SNIFITs and LUCIDs. Methods Mol Biol 2017; 1596:101-117. [PMID: 28293883 DOI: 10.1007/978-1-4939-6940-1_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Biosensors are used in many fields to measure the concentration of analytes, both in a cellular context and in human samples for medical care. Here, we outline the design of two types of modular biosensors: SNAP-tag-based indicators with a Fluorescent Intramolecular Tether (SNIFITs) and LUCiferase-based Indicators of Drugs (LUCIDs). These semisynthetic biosensors quantitatively measure analyte concentrations in vitro and on cell surfaces by an intramolecular competitive mechanism. We provide an overview of how to design and apply SNIFITs and LUCIDs.
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Affiliation(s)
- Helen Farrants
- National Centre of Competence in Research (NCCR) Chemical Biology, Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, École Polytechnique Fédéralede Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Julien Hiblot
- National Centre of Competence in Research (NCCR) Chemical Biology, Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, École Polytechnique Fédéralede Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Rudolf Griss
- National Centre of Competence in Research (NCCR) Chemical Biology, Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, École Polytechnique Fédéralede Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Kai Johnsson
- National Centre of Competence in Research (NCCR) Chemical Biology, Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, École Polytechnique Fédéralede Lausanne (EPFL), 1015, Lausanne, Switzerland.
- Max-Planck Institute for Medical Research, Department of Chemical Biology, 69120, Heidelberg, Germany.
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29
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NISHI S, YAMAMOTO C, YONEDA S, SUEDA S. Labeling of Cytoskeletal Proteins in Living Cells Using Biotin Ligase Carrying a Fluorescent Protein. ANAL SCI 2017; 33:897-902. [DOI: 10.2116/analsci.33.897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sairi NISHI
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | - Chihiro YAMAMOTO
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | - Sawako YONEDA
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | - Shinji SUEDA
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
- Research Center for Bio-microsensing Technology, Kyushu Institute of Technology
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30
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Kallemeijn WW, Scheij S, Voorn-Brouwer TM, Witte MD, Verhoek M, Overkleeft HS, Boot RG, Aerts JMFG. Endo-β-Glucosidase Tag Allows Dual Detection of Fusion Proteins by Fluorescent Mechanism-Based Probes and Activity Measurement. Chembiochem 2016; 17:1698-704. [PMID: 27383447 DOI: 10.1002/cbic.201600312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 11/07/2022]
Abstract
β-Glucoside-configured cyclophellitols are activity-based probes (ABPs) that allow sensitive detection of β-glucosidases. Their applicability to detect proteins fused with β-glucosidase was investigated in the cellular context. The tag was Rhodococcus sp. M-777 endoglycoceramidase II (EGCaseII), based on its lack of glycans and ability to hydrolyze fluorogenic 4-methylumbelliferyl β-d-lactoside (an activity absent in mammalian cells). Specific dual detection of fusion proteins was possible in vitro and in situ by using fluorescent ABPs and a fluorogenic substrate. Pre-blocking with conduritol β-epoxide (a poor inhibitor of EGCaseII) eliminated ABP labeling of endogenous β-glucosidases. ABPs equipped with biotin allowed convenient purification of the fusion proteins. Diversification of ABPs (distinct fluorophores, fluorogenic high-resolution detection moieties) should assist further research in living cells and organisms.
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Affiliation(s)
- Wouter W Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL
| | - Saskia Scheij
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, NL
| | - Tineke M Voorn-Brouwer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, NL
| | - Martin D Witte
- Department of Bio-Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, NL.,Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL
| | - Marri Verhoek
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL
| | - Hermen S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL
| | - Rolf G Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, NL.
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Gao F, Gao T, Zhou K, Zeng W. Small Molecule-Photoactive Yellow Protein Labeling Technology in Live Cell Imaging. Molecules 2016; 21:molecules21091163. [PMID: 27589715 PMCID: PMC6273459 DOI: 10.3390/molecules21091163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
Characterization of the chemical environment, movement, trafficking and interactions of proteins in live cells is essential to understanding their functions. Labeling protein with functional molecules is a widely used approach in protein research to elucidate the protein location and functions both in vitro and in live cells or in vivo. A peptide or a protein tag fused to the protein of interest and provides the opportunities for an attachment of small molecule probes or other fluorophore to image the dynamics of protein localization. Here we reviewed the recent development of no-wash small molecular probes for photoactive yellow protein (PYP-tag), by the means of utilizing a quenching mechanism based on the intramolecular interactions, or an environmental-sensitive fluorophore. Several fluorogenic probes have been developed, with fast labeling kinetics and cell permeability. This technology allows quick live-cell imaging of cell-surface and intracellular proteins without a wash-out procedure.
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Affiliation(s)
- Feng Gao
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
- The Third Xiangya Hospital, Central South University, Changsha 410013, China.
| | - Tang Gao
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
| | - Kechao Zhou
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
| | - Wenbin Zeng
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
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Naganbabu M, Perkins LA, Wang Y, Kurish J, Schmidt BF, Bruchez MP. Multiexcitation Fluorogenic Labeling of Surface, Intracellular, and Total Protein Pools in Living Cells. Bioconjug Chem 2016; 27:1525-31. [PMID: 27159569 PMCID: PMC4911959 DOI: 10.1021/acs.bioconjchem.6b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Malachite
green (MG) is a fluorogenic dye that shows fluorescence enhancement
upon binding to its engineered cognate protein, a fluorogen activating
protein (FAP). Energy transfer donors such as cyanine and rhodamine
dyes have been conjugated with MG to modify the spectral properties
of the fluorescent complexes, where the donor dyes transfer energy
through Förster resonance energy transfer to the MG complex
resulting in binding-conditional fluorescence emission in the far-red
region. In this article, we use a violet-excitable dye as a donor
to sensitize the far-red emission of the MG-FAP complex. Two blue
emitting fluorescent coumarin dyes were coupled to MG and evaluated
for energy transfer to the MG-FAP complex via its secondary excitation
band. 6,8-Difluoro-7-hydroxycoumarin-3-carboxylic acid (Pacific blue,
PB) showed the most efficient energy transfer and maximum brightness
in the far-red region upon violet (405 nm) excitation. These blue-red
(BluR) tandem dyes are spectrally varied from other tandem dyes and
are able to produce fluorescence images of the MG-FAP complex with
a large Stokes shift (>250 nm). These dyes are cell-permeable and
are used to label intracellular proteins. Used together with a cell-impermeable
hexa-Cy3-MG (HCM) dye that labels extracellular proteins, we are able
to visualize extracellular, intracellular, and total pools of cellular
protein using one fluorogenic tag that combines with distinct dyes
to effect different spectral characteristics.
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Affiliation(s)
- Matharishwan Naganbabu
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Lydia A Perkins
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Yi Wang
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Jeffery Kurish
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Brigitte F Schmidt
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Marcel P Bruchez
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
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33
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Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 2015; 11:917-23. [PMID: 26575238 DOI: 10.1038/nchembio.1959] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022]
Abstract
The past 20 years have witnessed the advent of numerous technologies to specifically and covalently label proteins in cellulo and in vivo with synthetic probes. These technologies range from self-labeling proteins tags to non-natural amino acids, and the question is no longer how we can specifically label a given protein but rather with what additional functionality we wish to equip it. In addition, progress in fields such as super-resolution microscopy and genome editing have either provided additional motivation to label proteins with advanced synthetic probes or removed some of the difficulties of conducting such experiments. By focusing on two particular applications, live-cell imaging and the generation of reversible protein switches, we outline the opportunities and challenges of the field and how the synergy between synthetic chemistry and protein engineering will make it possible to conduct experiments that are not feasible with conventional approaches.
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Walker CL, Lukyanov KA, Yampolsky IV, Mishin AS, Bommarius AS, Duraj-Thatte AM, Azizi B, Tolbert LM, Solntsev KM. Fluorescence imaging using synthetic GFP chromophores. Curr Opin Chem Biol 2015; 27:64-74. [DOI: 10.1016/j.cbpa.2015.06.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023]
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Affiliation(s)
- Christopher S von Bartheld
- Department of Physiology and Cell Biology, Center of Biomedical Research Excellence in Cell Biology, University of Nevada School of Medicine, Mailstop 352, Reno, NV, 89557, USA,
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