1
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Lu K, Wazawa T, Matsuda T, Shcherbakova DM, Verkhusha VV, Nagai T. Near-infrared PAINT localization microscopy via chromophore replenishment of phytochrome-derived fluorescent tag. Commun Biol 2024; 7:473. [PMID: 38637683 PMCID: PMC11026395 DOI: 10.1038/s42003-024-06169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Bacterial phytochromes are attractive molecular templates for engineering fluorescent proteins (FPs) because their near-infrared (NIR) emission significantly extends the spectral coverage of GFP-like FPs. Existing phytochrome-based FPs covalently bind heme-derived tetrapyrrole chromophores and exhibit constitutive fluorescence. Here we introduce Rep-miRFP, an NIR imaging probe derived from bacterial phytochrome, which interacts non-covalently and reversibly with biliverdin chromophore. In Rep-miRFP, the photobleached non-covalent adduct can be replenished with fresh biliverdin, restoring fluorescence. By exploiting this chromophore renewal capability, we demonstrate NIR PAINT nanoscopy in mammalian cells using Rep-miRFP.
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Affiliation(s)
- Kai Lu
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Tetsuichi Wazawa
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Tomoki Matsuda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Daria M Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vladislav V Verkhusha
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
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2
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Štefl M, Takamiya M, Middel V, Tekpınar M, Nienhaus K, Beil T, Rastegar S, Strähle U, Nienhaus GU. Caveolae disassemble upon membrane lesioning and foster cell survival. iScience 2024; 27:108849. [PMID: 38303730 PMCID: PMC10831942 DOI: 10.1016/j.isci.2024.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/22/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
Repair of lesions in the plasma membrane is key to sustaining cellular homeostasis. Cells maintain cytoplasmic as well as membrane-bound stores of repair proteins that can rapidly precipitate at the site of membrane lesions. However, little is known about the origins of lipids and proteins for resealing and repair of the plasma membrane. Here we study the dynamics of caveolar proteins after laser-induced lesioning of plasma membranes of mammalian C2C12 tissue culture cells and muscle cells of intact zebrafish embryos. Single-molecule diffusivity measurements indicate that caveolar clusters break up into smaller entities after wounding. Unlike Annexins and Dysferlin, caveolar proteins do not accumulate at the lesion patch. In caveolae-depleted cavin1a knockout zebrafish embryos, lesion patch formation is impaired, and injured cells show reduced survival. Our data suggest that caveolae disassembly releases surplus plasma membrane near the lesion to facilitate membrane repair after initial patch formation for emergency sealing.
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Affiliation(s)
- Martin Štefl
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
| | - Volker Middel
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
| | - Miyase Tekpınar
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Tanja Beil
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Strasse 1, 76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), PO Box 3640, 76021 Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, IL 61801, USA
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3
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Jeong S, Koh D, Gwak E, Srambickal CV, Seo D, Widengren J, Lee JC. Pushing the Resolution Limit of Stimulated Emission Depletion Optical Nanoscopy. Int J Mol Sci 2023; 25:26. [PMID: 38203197 PMCID: PMC10779414 DOI: 10.3390/ijms25010026] [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: 09/15/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and attain new insights into nanoscopic structures and processes that were previously inaccessible. In recent decades, numerous studies have endeavored to enhance super-resolution microscopy in terms of its spatial (lateral) resolution, axial resolution, and temporal resolution. In this review, we discuss recent efforts to push the resolution limit of stimulated emission depletion (STED) optical nanoscopy across multiple dimensions, including lateral resolution, axial resolution, temporal resolution, and labeling precision. We introduce promising techniques and methodologies building on the STED concept that have emerged in the field, such as MINSTED, isotropic STED, and event-triggered STED, and evaluate their respective strengths and limitations. Moreover, we discuss trade-off relationships that exist in far-field optical microscopy and how they come about in STED optical nanoscopy. By examining the latest developments addressing these aspects, we aim to provide an updated overview of the current state of STED nanoscopy and its potential for future research.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Dongbin Koh
- School of Undergraduate Studies, DGIST, Daegu 42988, Republic of Korea
| | - Eunha Gwak
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Chinmaya V. Srambickal
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jerker Widengren
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
- New Biology Research Center, DGIST, Daegu 42988, Republic of Korea
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4
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Yan J, Liu H, Wu Y, Niu B, Deng X, Zhang L, Dang Q, Wang Y, Lu X, Zhang B, Sun W. Recent progress of self-immobilizing and self-precipitating molecular fluorescent probes for higher-spatial-resolution imaging. Biomaterials 2023; 301:122281. [PMID: 37643487 DOI: 10.1016/j.biomaterials.2023.122281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Flourished in the past two decades, fluorescent probe technology provides researchers with accurate and efficient tools for in situ imaging of biomarkers in living cells and tissues and may play a significant role in clinical diagnosis and treatment such as biomarker detection, fluorescence imaging-guided surgery, and photothermal/photodynamic therapy. In situ imaging of biomarkers depends on the spatial resolution of molecular probes. Nevertheless, the majority of currently available molecular fluorescent probes suffer from the drawback of diffusing from the target region. This leads to a rapid attenuation of the fluorescent signal over time and a reduction in spatial resolution. Consequently, the diffused fluorescent signal cannot accurately reflect the in situ information of the target. Self-immobilizing and self-precipitating molecular fluorescent probes can be used to overcome this problem. These probes ensure that the fluorescent signal remains at the location where the signal is generated for a long time. In this review, we introduce the development history of the two types of probes and classify them in detail according to different design strategies. In addition, we compare their advantages and disadvantages, summarize some representative studies conducted in recent years, and propose prospects for this field.
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Affiliation(s)
- Jiawei Yan
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Huanying Liu
- School of Mechanical and Power Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Yingxu Wu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Ben Niu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Xiaojing Deng
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Linhao Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Qi Dang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Yubo Wang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Xiao Lu
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Boyu Zhang
- College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China.
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, 116024, China.
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5
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Yao Z, Wang X, Liu J, Zhou S, Zhang Z, He S, Liu J, Wu C, Fang X. Photoswitchable semiconducting polymer dots for pattern encoding and superresolution imaging. Chem Commun (Camb) 2023; 59:2469-2472. [PMID: 36752148 DOI: 10.1039/d2cc06707b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two photoswitchable semiconducting polymers were synthesized by covalently incorporating photochromic dithienylethene (DTE) into the main chains. Small size polymer dots (Pdots) were prepared and showed dynamic photoswitching upon alternate light irradiation. By virtue of the tunable photoswitching properties, effective pattern encoding and superresolution imaging with a resolution of up to about 30 nm were achieved.
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Affiliation(s)
- Zihan Yao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xiaodong Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Jie Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Siyu Zhou
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Zhe Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Shuwen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Changfeng Wu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xiaofeng Fang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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6
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Hou YN, Ding WL, Jiang XX, Hu JL, Tan ZZ, Zhao KH. New Far-Red and Near-Infrared Fluorescent Phycobiliproteins with Excellent Brightness and Photostability. Chembiochem 2022; 23:e202200267. [PMID: 35811374 DOI: 10.1002/cbic.202200267] [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: 05/08/2022] [Revised: 07/10/2022] [Indexed: 11/11/2022]
Abstract
Far-red and near-infrared fluorescent proteins can be used as fluorescence biomarkers in the region of maximal transmission of most tissues and facilitate multiplexing. Recently, we reported the generation and properties of far-red and near-infrared fluorescent phycobiliproteins, termed BeiDou Fluorescent Proteins (BDFPs), which can covalently bind the more readily accessible biliverdin. Far-red BDFPs maximally fluoresce at ∼670 nm, while near-infrared BDFPs fluoresce at ∼710 nm. In this work, we molecularly evolved BDFPs as follows: (a) mutations L58Q, S68R and M81K of BDFPs, which can maximally enhance the effective brightness in vivo by 350 %; (b) minimization and monomerization of far-red BDFPs 2.1, 2.2, 2.3, and near-infrared BDFPs 2.4, 2.5 and 2.6. These newly developed BDFPs are remarkably brighter than the formerly reported far-red and near-infrared fluorescent proteins. Their advantages are demonstrated by biolabeling in mammalian cells using super-resolution microscopy.
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Affiliation(s)
- Ya-Nan Hou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Wen-Long Ding
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xiang-Xiang Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Ji-Ling Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zi-Zhu Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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7
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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8
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Jeong S, Widengren J, Lee JC. Fluorescent Probes for STED Optical Nanoscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 12:21. [PMID: 35009972 PMCID: PMC8746377 DOI: 10.3390/nano12010021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Progress in developing fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, is inseparable from the advancement in optical fluorescence microscopy. Super-resolution microscopy, or optical nanoscopy, overcame the far-field optical resolution limit, known as Abbe's diffraction limit, by taking advantage of the photophysical properties of fluorescent probes. Therefore, fluorescent probes for super-resolution microscopy should meet the new requirements in the probes' photophysical and photochemical properties. STED optical nanoscopy achieves super-resolution by depleting excited fluorophores at the periphery of an excitation laser beam using a depletion beam with a hollow core. An ideal fluorescent probe for STED nanoscopy must meet specific photophysical and photochemical properties, including high photostability, depletability at the depletion wavelength, low adverse excitability, and biocompatibility. This review introduces the requirements of fluorescent probes for STED nanoscopy and discusses the recent progress in the development of fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, for the STED nanoscopy. The strengths and the limitations of the fluorescent probes are analyzed in detail.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm 10691, Sweden;
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
- New Biology Research Center, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea
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9
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Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions. Methods Mol Biol 2021; 2350:191-227. [PMID: 34331287 DOI: 10.1007/978-1-0716-1593-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.
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10
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Bogdanov AM, Gorbachev DA, Zaitseva ER, Smirnov AY, Baleeva NS, Baranov MS. Lability of Stationary and Time-Resolved Optical Properties of the Conformationally Locked CFP Chromophore Derivative. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Xu Y, Xu R, Wang Z, Zhou Y, Shen Q, Ji W, Dang D, Meng L, Tang BZ. Recent advances in luminescent materials for super-resolution imaging via stimulated emission depletion nanoscopy. Chem Soc Rev 2021; 50:667-690. [DOI: 10.1039/d0cs00676a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent progress on STED fluorophores for super-resolution imaging and also their characteristics are outlined here, thus providing some guidelines to select proper probes and even develop new materials for super-resolution imaging via STED nanoscopy.
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Affiliation(s)
- Yanzi Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ruohan Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Zhi Wang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Yu Zhou
- Instrumental Analysis Center
- Xi'an Jiao Tong University
- Xi'an
- P. R. China
| | - Qifei Shen
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Wenchen Ji
- Department of Orthopedics
- the First Affiliated Hospital of Xi’an Jiaotong University
- P. R. China
| | - Dongfeng Dang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Lingjie Meng
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ben Zhong Tang
- Department of Chemistry
- The Hong Kong University of Science and Technology
- Clear Water Bay
- Kowloon
- P. R. China
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12
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Mamontova AV, Shakhov AM, Lukyanov KA, Bogdanov AM. Deciphering the Role of Positions 145 and 165 in Fluorescence Lifetime Shortening in the EGFP Variants. Biomolecules 2020; 10:biom10111547. [PMID: 33202759 PMCID: PMC7696298 DOI: 10.3390/biom10111547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
The bright ultimately short lifetime enhanced emitter (BrUSLEE) green fluorescent protein, which differs from the enhanced green fluorescent protein (EGFP) in three mutations, exhibits an extremely short fluorescence lifetime at a relatively high brightness. An important contribution to shortening the BrUSLEE fluorescence lifetime compared to EGFP is provided by the T65G substitution of chromophore-forming residue and the Y145M mutation touching the chromophore environment. Although the influence of the T65G mutation was studied previously, the role of the 145th position in determining the GFPs physicochemical characteristics remains unclear. In this work, we show that the Y145M substitution, both alone and in combination with the F165Y mutation, does not shorten the fluorescence lifetime of EGFP-derived mutants. Thus, the unlocking of Y145M as an important determinant of lifetime tuning is possible only cooperatively with mutations at position 65. We also show here that the introduction of a T65G substitution into EGFP causes complex photobehavior of the respective mutants in the lifetime domain, namely, the appearance of two fluorescent states with different lifetimes, preserved in any combination with the Y145M and F165Y substitutions.
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Affiliation(s)
- Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | | | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Correspondence:
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13
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Matlashov ME, Shcherbakova DM, Alvelid J, Baloban M, Pennacchietti F, Shemetov AA, Testa I, Verkhusha VV. A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales. Nat Commun 2020; 11:239. [PMID: 31932632 PMCID: PMC6957686 DOI: 10.1038/s41467-019-13897-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 12/03/2019] [Indexed: 11/09/2022] Open
Abstract
Bright monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags for multicolor microscopy and in vivo imaging. Here we apply rational design to engineer a complete set of monomeric NIR FPs, which are the brightest genetically encoded NIR probes. We demonstrate that the enhanced miRFP series of NIR FPs, which combine high effective brightness in mammalian cells and monomeric state, perform well in both nanometer-scale imaging with diffraction unlimited stimulated emission depletion (STED) microscopy and centimeter-scale imaging in mice. In STED we achieve ~40 nm resolution in live cells. In living mice we detect ~105 fluorescent cells in deep tissues. Using spectrally distinct monomeric NIR FP variants, we perform two-color live-cell STED microscopy and two-color imaging in vivo. Having emission peaks from 670 nm to 720 nm, the next generation of miRFPs should become versatile NIR probes for multiplexed imaging across spatial scales in different modalities.
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Affiliation(s)
- Mikhail E Matlashov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anton A Shemetov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, 10461, USA. .,Medicum, Faculty of Medicine, University of Helsinki, 00029, Helsinki, Finland.
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14
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Moron V, Marazzi M, Wanko M. Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore? J Chem Theory Comput 2019; 15:4228-4240. [PMID: 31146524 DOI: 10.1021/acs.jctc.9b00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.
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Affiliation(s)
- Victor Moron
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
| | - Marco Marazzi
- Department of Theoretical Chemical Biology , Institute of Physical Chemistry, KIT , Kaiserstrasse 12 , 76131 Karlsruhe , Germany
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares, Madrid , Spain
- "Andrés M. del Rı́o" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid , Spain
| | - Marius Wanko
- Nano-Bio Spectroscopy Group and ETSF, Dpto. Fisica de Materiales , Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC and DIPC , Av. Tolosa 72 , 20018 San Sebastián , Spain
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15
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Bernhardt M, Nicolas JD, Osterhoff M, Mittelstädt H, Reuss M, Harke B, Wittmeier A, Sprung M, Köster S, Salditt T. A beamline-compatible STED microscope for combined visible-light and X-ray studies of biological matter. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1144-1151. [PMID: 31274438 DOI: 10.1107/s1600577519004089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
A dedicated stimulated emission depletion (STED) microscope had been designed and implemented into the Göttingen Instrument for Nano-Imaging with X-rays (GINIX) at the synchrotron beamline P10 of the PETRA III storage ring (DESY, Hamburg). The microscope was installed on the same optical table used for X-ray holography and scanning small-angle X-ray scattering (SAXS). Scanning SAXS was implemented with the Kirkpatrick-Baez (KB) nano-focusing optics of GINIX, while X-ray holography used a combined KB and X-ray waveguide optical system for full-field projection recordings at a defocus position of the object. The STED optical axis was aligned (anti-)parallel to the focused synchrotron beam and was laterally displaced from the KB focus. This close proximity between the STED and the X-ray probe enabled in situ combined recordings on the same biological cell, tissue or any other biomolecular sample, using the same environment and mounting. Here, the instrumentation and experimental details of this correlative microscopy approach are described, as first published in our preceding work [Bernhardt et al. (2018), Nat. Commun. 9, 3641], and the capabilities of correlative STED microscopy, X-ray holography and scanning SAXS are illustrated by presenting additional datasets on cardiac tissue cells with labeled actin cytoskeleton.
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Affiliation(s)
- Marten Bernhardt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
| | - Jan David Nicolas
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
| | - Haugen Mittelstädt
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077 Göttingen, Germany
| | - Matthias Reuss
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077 Göttingen, Germany
| | - Benjamin Harke
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077 Göttingen, Germany
| | - Andrew Wittmeier
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 47c, D-22607 Hamburg, Germany
| | - Sarah Köster
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany
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16
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Fabritius A, Ng D, Kist AM, Erdogan M, Portugues R, Griesbeck O. Imaging-Based Screening Platform Assists Protein Engineering. Cell Chem Biol 2018; 25:1554-1561.e8. [PMID: 30220597 DOI: 10.1016/j.chembiol.2018.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/29/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022]
Abstract
Protein engineering involves generating and screening large numbers of variants for desired properties. While modern DNA technology has made it easy to create protein diversity on the DNA level, the selection and validation of candidate proteins from large libraries remains a challenge. We built a screening platform that integrates high-quality fluorescence-based image analysis and robotic picking of bacterial colonies. It allows tracking each individual colony in a large population and collecting quantitative information on library composition during the protein evolution process. We demonstrate the power of the screening platform by optimizing a dim far-red-emitting fluorescent protein whose brightness increased several fold using iterative cycles of mutagenesis and platform-based screening. The resulting protein variant mCarmine is useful for imaging cells and structures within live tissue as well as for molecular tagging. Overall, the platform presented provides powerful, flexible, and low-cost instrumentation to accelerate many fluorescence-based protein optimization projects.
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Affiliation(s)
- Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - David Ng
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Andreas Michael Kist
- Sensorimotor Control, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Mutlu Erdogan
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Ruben Portugues
- Sensorimotor Control, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany.
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17
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Canty L, Hariharan S, Liu Q, Haney SA, Andrews DW. Peak emission wavelength and fluorescence lifetime are coupled in far-red, GFP-like fluorescent proteins. PLoS One 2018; 13:e0208075. [PMID: 30485364 PMCID: PMC6261627 DOI: 10.1371/journal.pone.0208075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/12/2018] [Indexed: 11/25/2022] Open
Abstract
The discovery and use of fluorescent proteins revolutionized cell biology by allowing the visualization of proteins in living cells. Advances in fluorescent proteins, primarily through genetic engineering, have enabled more advanced analyses, including Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM) and the development of genetically encoded fluorescent biosensors. These fluorescence protein-based sensors are highly effective in cells grown in monolayer cultures. However, it is often desirable to use more complex models including tissue explants, organoids, xenografts, and whole animals. These types of samples have poor light penetration owing to high scattering and absorption of light by tissue. Far-red light with a wavelength between 650-900nm is less prone to scatter, and absorption by tissues and can thus penetrate more deeply. Unfortunately, there are few fluorescent proteins in this region of the spectrum, and they have sub-optimal fluorescent properties including low brightness and short fluorescence lifetimes. Understanding the relationships between the amino-acid sequences of far-red fluorescence proteins and their photophysical properties including peak emission wavelengths and fluorescence lifetimes would be useful in the design of new fluorescence proteins for this region of the spectrum. We used both site-directed mutagenesis and gene-shuffling between mScarlet and mCardinal fluorescence proteins to create new variants and assess their properties systematically. We discovered that for far-red, GFP-like proteins the emission maxima and fluorescence lifetime have a strong inverse correlation.
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Affiliation(s)
- Laura Canty
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Santosh Hariharan
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Qian Liu
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Steven A. Haney
- Department of Oncology and Translational Research, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - David W. Andrews
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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18
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Wannier TM, Gillespie SK, Hutchins N, McIsaac RS, Wu SY, Shen Y, Campbell RE, Brown KS, Mayo SL. Monomerization of far-red fluorescent proteins. Proc Natl Acad Sci U S A 2018; 115:E11294-E11301. [PMID: 30425172 PMCID: PMC6275547 DOI: 10.1073/pnas.1807449115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Anthozoa-class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (λem ∼ 600-700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light in this range. A barrier to the use of naturally occurring RFP variants as molecular markers is that all are tetrameric, which is not ideal for cell biological applications. Efforts to engineer monomeric RFPs have typically produced dimmer and blue-shifted variants because the chromophore is sensitive to small structural perturbations. In fact, despite much effort, only four native RFPs have been successfully monomerized, leaving the majority of RFP biodiversity untapped in biomarker development. Here we report the generation of monomeric variants of HcRed and mCardinal, both far-red dimers, and describe a comprehensive methodology for the monomerization of red-shifted oligomeric RFPs. Among the resultant variants is mKelly1 (emission maximum, λem = 656 nm), which, along with the recently reported mGarnet2 [Matela G, et al. (2017) Chem Commun (Camb) 53:979-982], forms a class of bright, monomeric, far-red FPs.
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Affiliation(s)
- Timothy M Wannier
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Sarah K Gillespie
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Nicholas Hutchins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - R Scott McIsaac
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Chemistry, The University of Tokyo, 113-0033 Tokyo, Japan
| | - Kevin S Brown
- Department of Chemical and Biomedical Engineering, University of Connecticut, Storrs, CT 06269
- Department of Physics, University of Connecticut, Storrs, CT 06269
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
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19
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Kostyuk AI, Panova AS, Bilan DS, Belousov VV. Redox biosensors in a context of multiparameter imaging. Free Radic Biol Med 2018; 128:23-39. [PMID: 29630928 DOI: 10.1016/j.freeradbiomed.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
A wide variety of genetically encoded fluorescent biosensors are available to date. Some of them have already contributed significantly to our understanding of biological processes occurring at cellular and organismal levels. Using such an approach, outstanding success has been achieved in the field of redox biology. The probes allowed researchers to observe, for the first time, the dynamics of important redox parameters in vivo during embryogenesis, aging, the inflammatory response, the pathogenesis of various diseases, and many other processes. Given the differences in the readout and spectra of the probes, they can be used in multiparameter imaging in which several processes are monitored simultaneously in the cell. Intracellular processes form an extensive network of interactions. For example, redox changes are often accompanied by changes in many other biochemical reactions related to cellular metabolism and signaling. Therefore, multiparameter imaging can provide important information concerning the temporal and spatial relationship of various signaling and metabolic processes. In this review, we will describe the main types of genetically encoded biosensors, the most frequently used readout, and their use in multiplexed imaging mode.
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Affiliation(s)
- Alexander I Kostyuk
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anastasiya S Panova
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Institute for Cardiovascular Physiology, Georg August University Göttingen, Göttingen D-37073, Germany.
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20
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Kamper M, Ta H, Jensen NA, Hell SW, Jakobs S. Near-infrared STED nanoscopy with an engineered bacterial phytochrome. Nat Commun 2018; 9:4762. [PMID: 30420676 PMCID: PMC6232180 DOI: 10.1038/s41467-018-07246-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 10/17/2018] [Indexed: 01/18/2023] Open
Abstract
The near infrared (NIR) optical window between the cutoff for hemoglobin absorption at 650 nm and the onset of increased water absorption at 900 nm is an attractive, yet largely unexplored, spectral regime for diffraction-unlimited super-resolution fluorescence microscopy (nanoscopy). We developed the NIR fluorescent protein SNIFP, a bright and photostable bacteriophytochrome, and demonstrate its use as a fusion tag in live-cell microscopy and STED nanoscopy. We further demonstrate dual color red-confocal/NIR-STED imaging by co-expressing SNIFP with a conventional red fluorescent protein.
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Affiliation(s)
- Maria Kamper
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Haisen Ta
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nickels A Jensen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. .,Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.
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21
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Affiliation(s)
- Pieter E. Oomen
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
| | - Mohaddeseh A. Aref
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
| | - Ibrahim Kaya
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, 43180 Mölndal, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Nhu T. N. Phan
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
- University of Göttingen Medical Center, Institute of Neuro- and Sensory Physiology, Göttingen 37073, Germany
| | - Andrew G. Ewing
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
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22
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Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb) 2018; 10:516-526. [PMID: 30094420 PMCID: PMC6141309 DOI: 10.1039/c8ib00103k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics. In this report, a microfluidic sorter that discriminates members of a cell-based library based on their excited state lifetime and fluorescence intensity is used for the directed evolution of the photo-physical properties of FusionRed. In-flow measurements of the fluorescence lifetime are performed in a frequency-domain approach with sub-millisecond sampling times. Promising clones are sorted by optical force trapping with an infrared laser. Using this microfluidic sorter, mutants are generated with longer lifetimes than their precursor, FusionRed. This improvement in the excited state lifetime of the mutants leads to an increase in their fluorescence quantum yield up to 1.8-fold. In the course of evolution, we also identified one key mutation (L177M), which generated a mutant (FusionRed-M) that displayed ∼2-fold higher brightness than its precursor upon expression in mammalian (HeLa) cells. Photo-physical and mutational analyses of clones isolated at the different stages of mutagenesis reveal the photo-physical evolution towards higher in vivo brightness.
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Affiliation(s)
- Premashis Manna
- JILA, NIST and University of Colorado, Boulder, Colorado 80309, USA.
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23
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Bernhardt M, Nicolas JD, Osterhoff M, Mittelstädt H, Reuss M, Harke B, Wittmeier A, Sprung M, Köster S, Salditt T. Correlative microscopy approach for biology using X-ray holography, X-ray scanning diffraction and STED microscopy. Nat Commun 2018; 9:3641. [PMID: 30194418 PMCID: PMC6128893 DOI: 10.1038/s41467-018-05885-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
We present a correlative microscopy approach for biology based on holographic X-ray imaging, X-ray scanning diffraction, and stimulated emission depletion (STED) microscopy. All modalities are combined into the same synchrotron endstation. In this way, labeled and unlabeled structures in cells are visualized in a complementary manner. We map out the fluorescently labeled actin cytoskeleton in heart tissue cells and superimpose the data with phase maps from X-ray holography. Furthermore, an array of local far-field diffraction patterns is recorded in the regime of small-angle X-ray scattering (scanning SAXS), which can be interpreted in terms of biomolecular shape and spatial correlations of all contributing scattering constituents. We find that principal directions of anisotropic diffraction patterns coincide to a certain degree with the actin fiber directions and that actin stands out in the phase maps from holographic recordings. In situ STED recordings are proposed to formulate models for diffraction data based on co-localization constraints.
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Affiliation(s)
- M Bernhardt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - J-D Nicolas
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - M Osterhoff
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - H Mittelstädt
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - M Reuss
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - B Harke
- Abberior Instruments, Hans-Adolf-Krebs-Weg 1, D-37077, Göttingen, Germany
| | - A Wittmeier
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - M Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 47c, D-22607, Hamburg, Germany
| | - S Köster
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
| | - T Salditt
- Institut für Röntgenphysik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany.
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24
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Mamontova AV, Solovyev ID, Savitsky AP, Shakhov AМ, Lukyanov KA, Bogdanov AM. Bright GFP with subnanosecond fluorescence lifetime. Sci Rep 2018; 8:13224. [PMID: 30185895 PMCID: PMC6125319 DOI: 10.1038/s41598-018-31687-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) measures fluorescence decay rate at every pixel of an image. FLIM can separate probes of the same color but different fluorescence lifetimes (FL), thus it is a promising approach for multiparameter imaging. However, available GFP-like fluorescent proteins (FP) possess a narrow range of FLs (commonly, 2.3-3.5 ns) which limits their applicability for multiparameter FLIM. Here we report a new FP probe showing both subnanosecond fluorescence lifetime and exceptional fluorescence brightness (80% of EGFP). To design this probe we applied semi-rational amino acid substitutions selection. Critical positions (Thr65, Tyr145, Phe165) were altered based on previously reported effect on FL or excited state electron transfer. The resulting EGFP triple mutant, BrUSLEE (Bright Ultimately Short Lifetime Enhanced Emitter), allows for both reliable detection of the probe and recording FL signal clearly distinguishable from that of the spectrally similar commonly used GFPs. We demonstrated high performance of this probe in multiparameter FLIM experiment. We suggest that amino acid substitutions described here lead to a significant shift in radiative and non-radiative excited state processes equilibrium.
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Affiliation(s)
| | - Ilya D Solovyev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander P Savitsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander М Shakhov
- Semenov Institute of Chemical Physics, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | | | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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25
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Kleeman B, Olsson A, Newkold T, Kofron M, DeLay M, Hildeman D, Grimes HL. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry A 2018; 93:556-562. [PMID: 29533508 PMCID: PMC8008483 DOI: 10.1002/cyto.a.23360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/11/2022]
Abstract
The advent of facile genome engineering technologies has made the generation of knock-in gene-expression or fusion-protein reporters more tractable. Fluorescent protein labeling of specific genes combined with surface marker profiling can more specifically identify a cell population. However, the question of which fluorescent proteins to utilize to generate reporter constructs is made difficult by the number of candidate proteins and the lack of updated experimental data on newer fluorescent proteins. Compounding this problem, most fluorescent proteins are designed and tested for use in microscopy. To address this, we cloned and characterized the detection sensitivity, spectral overlap, and spillover spreading of 13 monomeric fluorescent proteins to determine utility in multicolor panels. We identified a group of five fluorescent proteins with high signal to noise ratio, minimal spectral overlap, and low spillover spreading making them compatible for multicolor experiments. Specifically, generating reporters with combinations of three of these proteins would allow efficient measurements even at low-level expression. Because the proteins are monomeric, they could function either as gene-expression or as fusion-protein reporters. Additionally, this approach can be generalized as new fluorescent proteins are developed to determine their usefulness in multicolor panels. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Benjamin Kleeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Tess Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matt Kofron
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - David Hildeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Gao H, Zhao X, Chen S. AIEgen-Based Fluorescent Nanomaterials: Fabrication and Biological Applications. Molecules 2018; 23:E419. [PMID: 29443927 PMCID: PMC6017469 DOI: 10.3390/molecules23020419] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
In recent years, luminogens with the feature of aggregation-induced emission (AIEgen) have emerged as advanced luminescent materials for fluorescent nanomaterial preparation. AIEgen-based nanomaterials show enhanced fluorescence efficiency and superior photostability, which thusly offer unique advantages in biological applications. In this review, we will summarize the fabrication methods of AIEgen-based nanomaterials and their applications in in vitro/in vivo imaging, cell tracing, photodynamic therapy and drug delivery, focusing on the recent progress.
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Affiliation(s)
- Hui Gao
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China.
| | - Xin Zhao
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China.
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Vicidomini G, Bianchini P, Diaspro A. STED super-resolved microscopy. Nat Methods 2018; 15:173-182. [DOI: 10.1038/nmeth.4593] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022]
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Fang X, Chen X, Li R, Liu Z, Chen H, Sun Z, Ju B, Liu Y, Zhang SXA, Ding D, Sun Y, Wu C. Multicolor Photo-Crosslinkable AIEgens toward Compact Nanodots for Subcellular Imaging and STED Nanoscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702128. [PMID: 28898567 DOI: 10.1002/smll.201702128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Aggregation induced emission (AIE) has attracted considerable interest for the development of fluorescence probes. However, controlling the bioconjugation and cellular labeling of AIE dots is a challenging problem. Here, this study reports a general approach for preparing small and bioconjugated AIE dots for specific labeling of cellular targets. The strategy is based on the synthesis of oxetane-substituted AIEgens to generate compact and ultrastable AIE dots via photo-crosslinking. A small amount of polymer enriched with oxetane groups is cocondensed with most of the AIEgens to functionalize the nanodot surface for subsequent streptavidin bioconjugation. Due to their small sizes, good stability, and surface functionalization, the cell-surface markers and subcellular structures are specifically labeled by the AIE dot bioconjugates. Remarkably, stimulated emission depletion imaging with AIE dots is achieved for the first time, and the spatial resolution is significantly enhanced to ≈95 nm. This study provides a general approach for small functional molecules for preparing small sized and ultrastable nanodots.
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Affiliation(s)
- Xiaofeng Fang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Xuanze Chen
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Rongqin Li
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhihe Liu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Haobin Chen
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Zezhou Sun
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, China
| | - Bo Ju
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yifei Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | | | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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