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Tsao KK, Imai S, Chang M, Hario S, Terai T, Campbell RE. The best of both worlds: Chemigenetic fluorescent sensors for biological imaging. Cell Chem Biol 2024:S2451-9456(24)00322-2. [PMID: 39236713 DOI: 10.1016/j.chembiol.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
Synthetic-based fluorescent chemosensors and protein-based fluorescent biosensors are two well-established classes of tools for visualizing and monitoring biological processes in living tissues. Chemigenetic sensors, created using a combination of both synthetic parts and protein parts, are an emerging class of tools that aims to combine the strengths, and overcome the drawbacks, of traditional chemosensors and biosensors. This review will survey the landscape of strategies used for fluorescent chemigenetic sensor design. These strategies include: attachment of synthetic elements to proteins using in vitro protein conjugation; attachment of synthetic elements to proteins using autonomous protein labeling; and translational incorporation of unnatural amino acids.
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Affiliation(s)
- Kelvin K Tsao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shosei Imai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Michael Chang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Saaya Hario
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuya Terai
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Robert E Campbell
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; CERVO, Brain Research Center and Department of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Québec, QC G1J 2G3, Canada.
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2
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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Macias-Contreras M, He H, Zhu L. Beyond O6-Benzylguanine: O6-(5-Pyridylmethyl)guanine as a Substrate for the Self-Labeling Enzyme SNAP-Tag. Bioconjug Chem 2018; 29:4104-4109. [DOI: 10.1021/acs.bioconjchem.8b00703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Huan He
- College of Medicine, Florida State University, Tallahassee, Florida 32306-4300, United States
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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Wang A, Feng J, Li Y, Zou P. Beyond Fluorescent Proteins: Hybrid and Bioluminescent Indicators for Imaging Neural Activities. ACS Chem Neurosci 2018; 9:639-650. [PMID: 29482322 DOI: 10.1021/acschemneuro.7b00455] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Optical biosensors have been invaluable tools in neuroscience research, as they provide the ability to directly visualize neural activity in real time, with high specificity, and with exceptional spatial and temporal resolution. Notably, a majority of these sensors are based on fluorescent protein scaffolds, which offer the ability to target specific cell types or even subcellular compartments. However, fluorescent proteins are intrinsically bulky tags, often insensitive to the environment, and always require excitation light illumination. To address these limitations, there has been a proliferation of alternative sensor scaffolds developed in recent years, including hybrid sensors that combine the advantages of synthetic fluorophores and genetically encoded protein tags, as well as bioluminescent probes. While still in their early stage of development as compared with fluorescent protein-based sensors, these novel probes have offered complementary solutions to interrogate various aspects of neuronal communication, including transmitter release, changes in membrane potential, and the production of second messengers. In this Review, we discuss these important new developments with a particular focus on design strategies.
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Affiliation(s)
- Anqi Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Jiesi Feng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
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Caldwell ST, Cairns AG, Olson M, Chalmers S, Sandison M, Mullen W, McCarron JG, Hartley RC. Synthesis of an azido-tagged low affinity ratiometric calcium sensor. Tetrahedron 2015; 71:9571-9578. [PMID: 26709317 PMCID: PMC4660056 DOI: 10.1016/j.tet.2015.10.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Changes in high localised concentrations of Ca2+ ions are fundamental to cell signalling. The synthesis of a dual excitation, ratiometric calcium ion sensor with a Kd of 90 μM, is described. It is tagged with an azido group for bioconjugation, and absorbs in the blue/green and emits in the red region of the visible spectrum with a large Stokes shift. The binding modulating nitro group is introduced to the BAPTA core prior to construction of a benzofuran-2-yl carboxaldehyde by an allylation–oxidation–cyclisation sequence, which is followed by condensation with an azido-tagged thiohydantoin. The thiohydantoin unit has to be protected with an acetoxymethyl (AM) caging group to allow CuAAC click reaction and incorporation of the KDEL peptide endoplasmic reticulum (ER) retention sequence.
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Affiliation(s)
- Stuart T Caldwell
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Andrew G Cairns
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Marnie Olson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Susan Chalmers
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Mairi Sandison
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - John G McCarron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Richard C Hartley
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
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Yan Q, Bruchez MP. Advances in chemical labeling of proteins in living cells. Cell Tissue Res 2015; 360:179-94. [PMID: 25743694 PMCID: PMC4380784 DOI: 10.1007/s00441-015-2145-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/02/2015] [Indexed: 01/07/2023]
Abstract
The pursuit of quantitative biological information via imaging requires robust labeling approaches that can be used in multiple applications and with a variety of detectable colors and properties. In addition to conventional fluorescent proteins, chemists and biologists have come together to provide a range of approaches that combine dye chemistry with the convenience of genetic targeting. This hybrid-tagging approach amalgamates the rational design of properties available through synthetic dye chemistry with the robust biological targeting available with genetic encoding. In this review, we discuss the current range of approaches that have been exploited for dye targeting or for targeting and activation and some of the recent applications that are uniquely permitted by these hybrid-tagging approaches.
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Affiliation(s)
- Qi Yan
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
| | - Marcel P. Bruchez
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
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Carter KP, Young AM, Palmer AE. Fluorescent sensors for measuring metal ions in living systems. Chem Rev 2014; 114:4564-601. [PMID: 24588137 PMCID: PMC4096685 DOI: 10.1021/cr400546e] [Citation(s) in RCA: 1540] [Impact Index Per Article: 154.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Kyle P. Carter
- Department
of Chemistry and
Biochemistry, BioFrontiers Institute, University
of Colorado, UCB 596,
3415 Colorado AvenueBoulder, Colorado 80303, United
States
| | - Alexandra M. Young
- Department
of Chemistry and
Biochemistry, BioFrontiers Institute, University
of Colorado, UCB 596,
3415 Colorado AvenueBoulder, Colorado 80303, United
States
| | - Amy E. Palmer
- Department
of Chemistry and
Biochemistry, BioFrontiers Institute, University
of Colorado, UCB 596,
3415 Colorado AvenueBoulder, Colorado 80303, United
States
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McCarron JG, Chalmers S, Olson ML, Girkin JM. Subplasma membrane Ca2+ signals. IUBMB Life 2012; 64:573-85. [PMID: 22653514 PMCID: PMC3638344 DOI: 10.1002/iub.1032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/24/2012] [Indexed: 12/03/2022]
Abstract
Ca2+ may selectively activate various processes in part by the cell's ability to localize changes in the concentration of the ion to specific subcellular sites. Interestingly, these Ca2+ signals begin most often at the plasma membrane space so that understanding subplasma membrane signals is central to an appreciation of local signaling. Several experimental procedures have been developed to study Ca2+ signals near the plasma membrane, but probably the most prevalent involve the use of fluorescent Ca2+ indicators and fall into two general approaches. In the first, the Ca2+ indicators themselves are specifically targeted to the subplasma membrane space to measure Ca2+ only there. Alternatively, the indicators are allowed to be dispersed throughout the cytoplasm, but the fluorescence emanating from the Ca2+ signals at the subplasma membrane space is selectively measured using high resolution imaging procedures. Although the targeted indicators offer an immediate appeal because of selectivity and ease of use, their limited dynamic range and slow response to changes in Ca2+ are a shortcoming. Use of targeted indicators is also largely restricted to cultured cells. High resolution imaging applied with rapidly responding small molecule Ca2+ indicators can be used in all cells and offers significant improvements in dynamic range and speed of response of the indicator. The approach is technically difficult, however, and realistic calibration of signals is not possible. In this review, a brief overview of local subplasma membrane Ca2+ signals and methods for their measurement is provided. © 2012 IUBMB IUBMB Life, 64(7): 573–585, 2012
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Affiliation(s)
- John G McCarron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK.
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10
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Switchable fluorophores for protein labeling in living cells. Curr Opin Chem Biol 2011; 15:768-74. [PMID: 22079663 DOI: 10.1016/j.cbpa.2011.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/11/2011] [Accepted: 10/17/2011] [Indexed: 12/20/2022]
Abstract
Numerous synthetic fluorophores have been developed that can switch their spectroscopic properties upon interaction with other molecules or by irradiation with light. In recent years, protein-labeling techniques have been introduced that permit the specific attachment of such molecules to proteins of interest in living cells. We review here how the attachment of switchable fluorophores to selected proteins of interest via self-labeling protein tags enables new applications in different areas of biology and discuss how these molecules could be further improved.
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Wombacher R, Cornish VW. Chemical tags: applications in live cell fluorescence imaging. JOURNAL OF BIOPHOTONICS 2011; 4:391-402. [PMID: 21567974 DOI: 10.1002/jbio.201100018] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/08/2011] [Accepted: 04/09/2011] [Indexed: 05/30/2023]
Abstract
Technologies to visualize cellular structures and dynamics enable cell biologists to gain insight into complex biological processes. Currently, fluorescent proteins are used routinely to investigate the behavior of proteins in live cells. Chemical biology techniques for selective labeling of proteins with fluorescent labels have become an attractive alternative to fluorescent protein labeling. In the last ten years the progress in the development of chemical tagging methods have been substantial offering a broad palette of applications for live cell fluorescent microscopy. Several methods for protein labeling have been established, using protein tags, peptide tags and enzyme mediated tagging. This review focuses on the different strategies to achieve the attachment of fluorophores to proteins in live cells and cast light on the advantages and disadvantages of each individual method. Selected experiments in which chemical tags have been successfully applied to live cell imaging will be discussed and evaluated.
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Hinner MJ, Johnsson K. How to obtain labeled proteins and what to do with them. Curr Opin Biotechnol 2010; 21:766-76. [PMID: 21030243 DOI: 10.1016/j.copbio.2010.09.011] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/10/2010] [Accepted: 09/21/2010] [Indexed: 12/20/2022]
Abstract
We review new and established methods for the chemical modification of proteins in living cells and highlight recent applications. The review focuses on tag-mediated protein labeling methods, such as the tetracysteine tag and SNAP-tag, and new developments in this field such as intracellular labeling with lipoic acid ligase. Recent promising advances in the incorporation of unnatural amino acids into proteins are also briefly discussed. We describe new tools using tag-mediated labeling methods including the super-resolution microscopy of tagged proteins, the study of the interactions of proteins and protein domains, the subcellular targeting of synthetic ion sensors, and the generation of new semisynthetic metabolite sensors. We conclude with a view on necessary future developments, with one example being the selective labeling of non-tagged, native proteins in complex protein mixtures.
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Affiliation(s)
- Marlon J Hinner
- Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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