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Budiarta M, Streit M, Beliu G. Site-specific protein labeling strategies for super-resolution microscopy. Curr Opin Chem Biol 2024; 80:102445. [PMID: 38490137 DOI: 10.1016/j.cbpa.2024.102445] [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: 01/14/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024]
Abstract
Super-resolution microscopy (SRM) has transformed our understanding of proteins' subcellular organization and revealed cellular details down to nanometers, far beyond conventional microscopy. While localization precision is independent of the number of fluorophores attached to a biomolecule, labeling density is a decisive factor for resolving complex biological structures. The average distance between adjacent fluorophores should be less than half the desired spatial resolution for optimal clarity. While this was not a major limitation in recent decades, the success of modern microscopy approaching molecular resolution down to the single-digit nanometer range will depend heavily on advancements in fluorescence labeling. This review highlights recent advances and challenges in labeling strategies for SRM, focusing on site-specific labeling technologies. These advancements are crucial for improving SRM precision and expanding our understanding of molecular interactions.
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Affiliation(s)
- Made Budiarta
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Gerti Beliu
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; Interdisciplinary Institute for Neuroscience, University of Bordeaux, CNRS, UMR 5297, 33076 Bordeaux, France.
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2
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Truong HM, Cruz-Colón KO, Martínez-Márquez JY, Willer JR, Travis AM, Biswas SK, Lo WK, Bolz HJ, Pearring JN. The tectonic complex regulates membrane protein composition in the photoreceptor cilium. Nat Commun 2023; 14:5671. [PMID: 37704658 PMCID: PMC10500017 DOI: 10.1038/s41467-023-41450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The primary cilium is a signaling organelle with a unique membrane composition maintained by a diffusional barrier residing at the transition zone. Many transition zone proteins, such as the tectonic complex, are linked to preserving ciliary composition but the mechanism remains unknown. To understand tectonic's role, we generate a photoreceptor-specific Tctn1 knockout mouse. Loss of Tctn1 results in the absence of the entire tectonic complex and associated MKS proteins yet has minimal effects on the transition zone structure of rod photoreceptors. We find that the protein composition of the photoreceptor cilium is disrupted as non-resident membrane proteins accumulate in the cilium over time, ultimately resulting in photoreceptor degeneration. We further show that fluorescent rhodopsin moves faster through the transition zone in photoreceptors lacking tectonic, which suggests that the tectonic complex acts as a physical barrier to slow down membrane protein diffusion in the photoreceptor transition zone to ensure proper removal of non-resident membrane proteins.
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Affiliation(s)
- Hanh M Truong
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kevin O Cruz-Colón
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Jason R Willer
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA
| | - Amanda M Travis
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA
| | - Sondip K Biswas
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Woo-Kuen Lo
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Hanno J Bolz
- Senckenberg Centre for Human Genetics, Frankfurt am Main, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Jillian N Pearring
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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3
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Eklund AS, Jungmann R. Optimized Coiled-Coil Interactions for Multiplexed Peptide-PAINT. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206347. [PMID: 36642829 DOI: 10.1002/smll.202206347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution microscopy has revolutionized how researchers characterize samples in the life sciences in the last decades. Amongst methods employing single-molecule localization microscopy, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a relatively easy-to-implement method that uses the programmable and repetitive binding of dye-labeled DNA imager strands to their respective docking strands. Recently developed Peptide-PAINT replaces the interaction of oligonucleotides by short coiled-coil peptide sequences leading to an improved labeling scheme by reducing linkage errors to target proteins. However, only one coiled-coil pair is currently available for Peptide-PAINT, preventing multiplexed imaging. In this study, the initial Peptide-PAINT E/K coil is improved by modifying its length for optimized binding kinetics leading to improved localization precisions. Additionally, an orthogonal P3/P4 coil pair is introduced, enabling 2-plex Peptide-PAINT imaging and benchmarking its performance and orthogonality using single-molecule and DNA origami assays. Finally, the P3/P4 peptide pair is used to image the human epidermal growth factor receptors 2 (ErbB2/Her2) in 2D and 3D at the single receptor level using genetically encoded peptide tags.
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Affiliation(s)
- Alexandra S Eklund
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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Tas RP, Albertazzi L, Voets IK. Small Peptide-Protein Interaction Pair for Genetically Encoded, Fixation Compatible Peptide-PAINT. NANO LETTERS 2021; 21:9509-9516. [PMID: 34757759 PMCID: PMC8631740 DOI: 10.1021/acs.nanolett.1c02895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/01/2021] [Indexed: 05/08/2023]
Abstract
Super-resolution microscopy via PAINT has been widely adopted in life sciences to interrogate the nanoscale architecture of many cellular structures. However, obtaining quantitative information in fixed cellular samples remains challenging because control of labeling stoichiometry is hampered in current approaches due to click-chemistry and additional targeting probes. To overcome these challenges, we have identified a small, PDZ-based, peptide-protein interaction pair that is genetically encodable and compatible with super-resolution imaging upon cellular fixation without additional labeling. Stoichiometric labeling control by genetic incorporation of this probe into the cellular vimentin network and mitochondria resulted in super-resolved 3D reconstructions with high specificity and spatial resolution. Further characterization reveals that this peptide-protein interaction is compatible with quantitative PAINT and that its binding kinetics remains unaltered upon fixation. Finally, by fusion of our probe to nanobodies against conventional expression markers, we show that this approach provides a versatile addition to the super-resolution toolbox.
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Affiliation(s)
- Roderick P. Tas
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory
of Nanoscopy for Nanomedicine, Institute for Complex Molecular Systems
and Department of Biomedical Engineering, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Ilja K. Voets
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [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: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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Putlyaeva LV, Lukyanov KA. Studying SARS-CoV-2 with Fluorescence Microscopy. Int J Mol Sci 2021; 22:6558. [PMID: 34207305 PMCID: PMC8234815 DOI: 10.3390/ijms22126558] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a powerful technology enabling detailed investigation of virus-cell interactions in fixed and live samples with high specificity. While spatial resolution of conventional fluorescence microscopy is not sufficient to resolve all virus-related structures, super-resolution fluorescence microscopy can solve this problem. In this paper, we review the use of fluorescence microscopy to study SARS-CoV-2 and related viruses. The prospects for the application of the recently developed advanced methods of fluorescence labeling and microscopy-which in our opinion can provide important information about the molecular biology of SARS-CoV-2-are discussed.
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Affiliation(s)
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
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Oi C, Mochrie SGJ, Horrocks MH, Regan L. PAINT using proteins: A new brush for super-resolution artists. Protein Sci 2020; 29:2142-2149. [PMID: 32949055 PMCID: PMC7586915 DOI: 10.1002/pro.3953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
PAINT (points accumulation for imaging in nanoscale topography) refers to methods that achieve the sparse temporal labeling required for super-resolution imaging by using transient interactions between a biomolecule of interest and a fluorophore. There have been a variety of different implementations of this method since it was first described in 2006. Recent papers illustrate how transient peptide-protein interactions, rather than small molecule binding or DNA oligonucleotide duplex formation, can be employed to perform PAINT-based single molecule localization microscopy (SMLM). We discuss the different approaches to PAINT using peptide and protein interactions, and their applications in vitro and in vivo. We highlight the important parameters to consider when selecting suitable peptide-protein interaction pairs for such studies. We also note the opportunities for protein scientists to apply their expertise in guiding the choice of peptide and protein pairs that are used. Finally, we discuss the potential for expanding super-resolution imaging methods based on transient peptide-protein interactions, including the development of simultaneous multicolor imaging of multiple proteins and the study of very high and very low abundance proteins in live cells.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
| | - Simon G. J. Mochrie
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of PhysicsYale UniversityNew HavenConnecticutUSA
| | | | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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Oi C, Gidden Z, Holyoake L, Kantelberg O, Mochrie S, Horrocks MH, Regan L. LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions. Commun Biol 2020; 3:458. [PMID: 32820217 PMCID: PMC7441314 DOI: 10.1038/s42003-020-01188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
We present LIVE-PAINT, a new approach to super-resolution fluorescent imaging inside live cells. In LIVE-PAINT only a short peptide sequence is fused to the protein being studied, unlike conventional super-resolution methods, which rely on directly fusing the biomolecule of interest to a large fluorescent protein, organic fluorophore, or oligonucleotide. LIVE-PAINT works by observing the blinking of localized fluorescence as this peptide is reversibly bound by a protein that is fused to a fluorescent protein. We have demonstrated the effectiveness of LIVE-PAINT by imaging a number of different proteins inside live S. cerevisiae. Not only is LIVE-PAINT widely applicable, easily implemented, and the modifications minimally perturbing, but we also anticipate it will extend data acquisition times compared to those previously possible with methods that involve direct fusion to a fluorescent protein.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
| | - Zoe Gidden
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Louise Holyoake
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Owen Kantelberg
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland
| | - Simon Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Mathew H Horrocks
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland.
| | - Lynne Regan
- Center for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland.
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