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Zuo J, Peng A, Wu P, Chen J, Yao C, Pan J, Zhu E, Weng Y, Zhang K, Feng H, Jin Z, Qian Z. Charge-regulated fluorescent anchors enable high-fidelity tracking of plasma membrane dynamics during biological events. Chem Sci 2024; 15:8934-8945. [PMID: 38873067 PMCID: PMC11168104 DOI: 10.1039/d4sc01423e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/04/2024] [Indexed: 06/15/2024] Open
Abstract
Many biological processes generally require long-term visualization tools for time-scale dynamic changes of the plasma membrane, but there is still a lack of design rules for such imaging tools based on small-molecule fluorescent probes. Herein, we revealed the key regulatory roles of charge number and species of fluorescent dyes in the anchoring ability of the plasma membrane and found that the introduction of multi-charged units and appropriate charge species is often required for fluorescent dyes with strong plasma membrane anchoring ability by systematically investigating the structure-function relationship of cyanostyrylpyridium (CSP) dyes with different charge numbers and species and their imaging performance for the plasma membrane. The CSP-DBO dye constructed exhibits strong plasma membrane anchoring ability in staining the plasma membrane of cells, in addition to many other advantages such as excellent biocompatibility and general universality of cell types. Such a fluorescent anchor has been successfully used to monitor chemically induced plasma membrane damage and dynamically track various cellular biological events such as cell fusion and cytokinesis over a long period of time by continuously monitoring the dynamic morphological changes of the plasma membrane, providing a valuable precise visualization tool to study the physiological response to chemical stimuli and reveal the structural morphological changes and functions of the plasma membrane during these important biological events from a dynamic perspective. Furthermore, CSP-DBO exhibits excellent biocompatibility and imaging capability in vivo such as labelling the plasma membrane in vivo and monitoring the metabolic process of lipofuscin as an aging indicator.
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Affiliation(s)
- Jiaqi Zuo
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Aohui Peng
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Penglei Wu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Junyi Chen
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Chuangye Yao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Junjun Pan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Engao Zhu
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Yingye Weng
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Kewei Zhang
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Hui Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Zhigang Jin
- College of Life Science, Zhejiang Normal University YIngbin Road 688 JInhua 321004 China
| | - Zhaosheng Qian
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
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2
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Zuo F, Jiang L, Su N, Zhang Y, Bao B, Wang L, Shi Y, Yang H, Huang X, Li R, Zeng Q, Chen Z, Lin Q, Zhuang Y, Zhao Y, Chen X, Zhu L, Yang Y. Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA. Nat Chem Biol 2024:10.1038/s41589-024-01629-x. [PMID: 38783134 DOI: 10.1038/s41589-024-01629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.
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Affiliation(s)
- Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Limei Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yajie Shi
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huimin Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ruilong Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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3
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Zhang Y, Xu Z, Xiao Y, Jiang H, Zuo X, Li X, Fang X. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Nat Commun 2024; 15:4206. [PMID: 38760339 PMCID: PMC11101630 DOI: 10.1038/s41467-024-48478-9] [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: 10/02/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.
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Affiliation(s)
- Yufan Zhang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China
| | - Zhonghe Xu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Xiao
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haodong Jiang
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Xing Li
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Xianyang Fang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics Chinese Academy of Sciences, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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4
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Krueger TD, Chen C, Fang C. Targeting Ultrafast Spectroscopic Insights into Red Fluorescent Proteins. Chem Asian J 2023; 18:e202300668. [PMID: 37682793 DOI: 10.1002/asia.202300668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/10/2023]
Abstract
Red fluorescent proteins (RFPs) represent an increasingly popular class of genetically encodable bioprobes and biomarkers that can advance next-generation breakthroughs across the imaging and life sciences. Since the rational design of RFPs with improved functions or enhanced versatility requires a mechanistic understanding of their working mechanisms, while fluorescence is intrinsically an ultrafast event, a suitable toolset involving steady-state and time-resolved spectroscopic techniques has become powerful in delineating key structural features and dynamic steps which govern irreversible photoconverting or reversible photoswitching RFPs, and large Stokes shift (LSS)RFPs. The pertinent cis-trans isomerization and protonation state change of RFP chromophores in their local environments, involving key residues in protein matrices, lead to rich and complicated spectral features across multiple timescales. In particular, ultrafast excited-state proton transfer in various LSSRFPs showcases the resolving power of wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in mapping a photocycle with crucial knowledge about the red-emitting species. Moreover, recent progress in noncanonical RFPs with a site-specifically modified chromophore provides an appealing route for efficient engineering of redder and brighter RFPs, highly desirable for bioimaging. Such an effective feedback loop involving physical chemists, protein engineers, and biomedical microscopists will enable future successes to expand fundamental knowledge and improve human health.
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Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon, 97331-4003, USA
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5
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Jiang L, Xie X, Su N, Zhang D, Chen X, Xu X, Zhang B, Huang K, Yu J, Fang M, Bao B, Zuo F, Yang L, Zhang R, Li H, Huang X, Chen Z, Zeng Q, Liu R, Lin Q, Zhao Y, Ren A, Zhu L, Yang Y. Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells. Nat Methods 2023; 20:1563-1572. [PMID: 37723244 DOI: 10.1038/s41592-023-01997-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/08/2023] [Indexed: 09/20/2023]
Abstract
Fluorescent RNAs, aptamers that bind and activate small fluorogenic dyes, have provided a particularly attractive approach to visualizing RNAs in live cells. However, the simultaneous imaging of multiple RNAs remains challenging due to a lack of bright and stable fluorescent RNAs with bio-orthogonality and suitable spectral properties. Here, we develop the Clivias, a series of small, monomeric and stable orange-to-red fluorescent RNAs with large Stokes shifts of up to 108 nm, enabling the simple and robust imaging of RNA with minimal perturbation of the target RNA's localization and functionality. In combination with Pepper fluorescent RNAs, the Clivias enable the single-excitation two-emission dual-color imaging of cellular RNAs and genomic loci. Clivias can also be used to detect RNA-protein interactions by bioluminescent imaging both in live cells and in vivo. We believe that these large Stokes shift fluorescent RNAs will be useful tools for the tracking and quantification of multiple RNAs in diverse biological processes.
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Affiliation(s)
- Li Jiang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Xie
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dasheng Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Fluorescence Diagnosis (Shanghai) Biotech Company Ltd, Shanghai, China
| | - Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bibi Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Kaiyi Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
- Department of Orthopedics Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jingwei Yu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Mengyue Fang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lipeng Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Huiwen Li
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinyi Huang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengda Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qingmei Zeng
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Department of Orthopedics Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Linyong Zhu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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6
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Winer L, Motiei L, Margulies D. Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates. Bioconjug Chem 2023; 34:1509-1522. [PMID: 37556353 PMCID: PMC10515487 DOI: 10.1021/acs.bioconjchem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/27/2023] [Indexed: 08/11/2023]
Abstract
The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.
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Affiliation(s)
- Lulu Winer
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - Leila Motiei
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - David Margulies
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
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7
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Bains J, Qureshi N, Ceylan B, Wacker A, Schwalbe H. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function. Nucleic Acids Res 2023; 51:e82. [PMID: 37409574 PMCID: PMC10450168 DOI: 10.1093/nar/gkad574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
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Affiliation(s)
- Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
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8
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Mizutani Y, Mizuno M. Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale. J Chem Phys 2022; 157:240901. [PMID: 36586981 DOI: 10.1063/5.0116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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9
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Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
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Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- *Correspondence: Mara Dierssen,
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10
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Yao X, Wuzhang K, Peng B, Chen T, Zhang Y, Liu H, Li L, Fu X, Tang K. Engineering the expression of plant secondary metabolites-genistein and scutellarin through an efficient transient production platform in Nicotiana benthamiana L. FRONTIERS IN PLANT SCIENCE 2022; 13:994792. [PMID: 36147222 PMCID: PMC9485999 DOI: 10.3389/fpls.2022.994792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Plant natural products (PNPs) are active substances indispensable to human health with a wide range of medical and commercial applications. However, excessive population growth, overexploitation of natural resources, and expensive total chemical synthesis have led to recurrent supply shortages. Despite the fact that the microbial production platform solved these challenges, the platform still has drawbacks such as environmental pollution, high costs, and non-green production. In this study, an efficient platform for the production of PNPs based on the transient expression system of Nicotiana benthamiana L. combined with synthetic biology strategies was developed. Subsequently, the feasibility of the platform was verified by a simple "test unit." This platform was used to synthesize two high-value PNPs: genistein (5.51 nmol g-1 FW) and scutellarin (11.35 nmol g-1 FW). Importantly, this is the first report on the synthesis of scutellarin in heterologous plants. The platform presented here will possibly be adopted for the heterologous production of genistein and scutellarin in tobacco plants as a novel and sustainable production strategy.
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11
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Affiliation(s)
- Theodorus W J Gadella
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy (LCAM), Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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12
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Ruthazer ES, Béïque JC, De Koninck Y. Editorial: Shedding Light on the Nervous System: Progress in Neurophotonics Research. Front Neural Circuits 2022; 16:901376. [PMID: 35664457 PMCID: PMC9156792 DOI: 10.3389/fncir.2022.901376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Edward S. Ruthazer
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- *Correspondence: Edward S. Ruthazer
| | - Jean-Claude Béïque
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Yves De Koninck
- Department of Psychiatry and Neuroscience, Institut Universitaire en santé mentale de Québec, Université Laval, Quebec City, QC, Canada
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13
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Bourque K, Hawey C, Jiang A, Mazarura GR, Hébert TE. Biosensor-based profiling to track cellular signalling in patient-derived models of dilated cardiomyopathy. Cell Signal 2022; 91:110239. [PMID: 34990783 DOI: 10.1016/j.cellsig.2021.110239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/18/2022]
Abstract
Dilated cardiomyopathies (DCM) represent a diverse group of cardiovascular diseases impacting the structure and function of the myocardium. To better treat these diseases, we need to understand the impact of such cardiomyopathies on critical signalling pathways that drive disease progression downstream of receptors we often target therapeutically. Our understanding of cellular signalling events has progressed substantially in the last few years, in large part due to the design, validation and use of biosensor-based approaches to studying such events in cells, tissues and in some cases, living animals. Another transformative development has been the use of human induced pluripotent stem cells (hiPSCs) to generate disease-relevant models from individual patients. We highlight the importance of going beyond monocellular cultures to incorporate the influence of paracrine signalling mediators. Finally, we discuss the recent coalition of these approaches in the context of DCM. We discuss recent work in generating patient-derived models of cardiomyopathies and the utility of using signalling biosensors to track disease progression and test potential therapeutic strategies that can be later used to inform treatment options in patients.
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Affiliation(s)
- Kyla Bourque
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Cara Hawey
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Alyson Jiang
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Grace R Mazarura
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada.
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14
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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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15
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Tam C, Zhang KYJ. FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins. Proteins 2021; 90:732-746. [PMID: 34676905 DOI: 10.1002/prot.26270] [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: 05/13/2021] [Revised: 09/19/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Fluorescent protein (FP) design is among the challenging protein design problems due to the tradeoffs among multiple properties to be optimized. Despite the accumulated efforts in design and characterization, progress has been slow in gaining a full understanding of sequence-property relationships to tackle the multiobjective design problem in FPs. In this study, we approach this problem by developing FPredX, a collection of gradient-boosted decision tree models, which mapped FP sequences to four major design targets of FPs, including excitation maximum, emission maximum, brightness, and oligomeric state. By training using one-hot encoded multiple aligned sequences with hyperparameters optimization in each model, FPredX models showed excellent prediction performance for all target properties compared with existing methods. We further interpreted the FPredX models by comparing the importance of positions along the aligned FP sequence to the predictive performance and suggested positions, which showed differential importance deemed by FPredX models to the prediction of each target property.
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Affiliation(s)
- Chunlai Tam
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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16
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Ruiz-Llorente L, Vega MC, Fernández FJ, Langa C, Morrell NW, Upton PD, Bernabeu C. Generation of a Soluble Form of Human Endoglin Fused to Green Fluorescent Protein. Int J Mol Sci 2021; 22:ijms222011282. [PMID: 34681942 PMCID: PMC8539536 DOI: 10.3390/ijms222011282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 01/06/2023] Open
Abstract
Endoglin (Eng, CD105) is a type I membrane glycoprotein that functions in endothelial cells as an auxiliary receptor for transforming growth factor β (TGF-β)/bone morphogenetic protein (BMP) family members and as an integrin ligand, modulating the vascular pathophysiology. Besides the membrane-bound endoglin, there is a soluble form of endoglin (sEng) that can be generated by the action of the matrix metalloproteinase (MMP)-14 or -12 on the juxtamembrane region of its ectodomain. High levels of sEng have been reported in patients with preeclampsia, hypercholesterolemia, atherosclerosis and cancer. In addition, sEng is a marker of cardiovascular damage in patients with hypertension and diabetes, plays a pathogenic role in preeclampsia, and inhibits angiogenesis and tumor proliferation, migration, and invasion in cancer. However, the mechanisms of action of sEng have not yet been elucidated, and new tools and experimental approaches are necessary to advance in this field. To this end, we aimed to obtain a fluorescent form of sEng as a new tool for biological imaging. Thus, we cloned the extracellular domain of endoglin in the pEGFP-N1 plasmid to generate a fusion protein with green fluorescent protein (GFP), giving rise to pEGFP-N1/Eng.EC. The recombinant fusion protein was characterized by transient and stable transfections in CHO-K1 cells using fluorescence microscopy, SDS-PAGE, immunodetection, and ELISA techniques. Upon transfection with pEGFP-N1/Eng.EC, fluorescence was readily detected in cells, indicating that the GFP contained in the recombinant protein was properly folded into the cytosol. Furthermore, as evidenced by Western blot analysis, the secreted fusion protein yielded the expected molecular mass and displayed a specific fluorescent signal. The fusion protein was also able to bind to BMP9 and BMP10 in vitro. Therefore, the construct described here could be used as a tool for functional in vitro studies of the extracellular domain of endoglin.
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Affiliation(s)
- Lidia Ruiz-Llorente
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
- Biochemistry and Molecular Biology Unit, Department of System Biology, School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
| | - Carmen Langa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (N.W.M.); (P.D.U.)
| | - Paul D. Upton
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (N.W.M.); (P.D.U.)
| | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (L.R.-L.); (M.C.V.); (F.J.F.); (C.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
- Correspondence:
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17
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The dynamic surface properties of green fluorescent protein and its mixtures with poly(N,N-diallyl-N-hexyl-N-methylammonium chloride). J Taiwan Inst Chem Eng 2021. [DOI: 10.1016/j.jtice.2021.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Kundu R, Chandra A, Datta A. Fluorescent Chemical Tools for Tracking Anionic Phospholipids. Isr J Chem 2021. [DOI: 10.1002/ijch.202100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rajasree Kundu
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Amitava Chandra
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
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19
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Bae Y, Lee SK, Chae YC, Park CY, Kang S. Accessibility-dependent topology studies of membrane proteins using a SpyTag/SpyCatcher protein-ligation system. Int J Biol Macromol 2021; 175:171-178. [PMID: 33549659 DOI: 10.1016/j.ijbiomac.2021.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/08/2023]
Abstract
Covalent protein-ligation methods were used not only to visualize the localization of proteins of interest in cells, but also to study the topology of plasma and subcellular organelle membrane proteins using fluorescent cell imaging. A 13-amino-acid SpyTag (ST) peptide was genetically introduced either into a variety of subcellular proteins of interest or into different positions of plasma or subcellular organelle membrane proteins individually. Conversely, a 15 kDa SpyCatcher (SC) protein was chemically conjugated with either fluorescent dyes or horseradish peroxidase (HRP) via a thiol-maleimide reaction. The extracellular ST-fused plasma membrane proteins were efficiently labeled with the fluorescent-dye-conjugated SC in both live and permeabilized cells, whereas the intracellularly localized ST-fused subcellular proteins were only labeled in permeabilized cells because of the limited accessibility of the fluorescent-dye-conjugated SC to the membrane. The fluorescent-dye-labeled SC together with selective membrane-permeabilizing agents successfully labeled the plasma or the subcellular organelle membrane proteins in a topology-dependent manner. Moreover, the HRP-conjugated SC not only successfully labeled the ST-fused plasma membrane proteins, thus significantly enhancing fluorescent signals in combination with the tyramide signal amplification agents, but also ligated with an external ST-fused target ligand, thus selectively binding to the endogenously expressed cellular receptors of the target cancer cells.
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Affiliation(s)
- Yoonji Bae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang Kwon Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chan Young Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sebyung Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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20
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Lee J, Liu Z, Suzuki PH, Ahrens JF, Lai S, Lu X, Guan S, St-Pierre F. Versatile phenotype-activated cell sorting. SCIENCE ADVANCES 2020; 6:6/43/eabb7438. [PMID: 33097540 PMCID: PMC7608836 DOI: 10.1126/sciadv.abb7438] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
Unraveling the genetic and epigenetic determinants of phenotypes is critical for understanding and re-engineering biology and would benefit from improved methods to separate cells based on phenotypes. Here, we report SPOTlight, a versatile high-throughput technique to isolate individual yeast or human cells with unique spatiotemporal profiles from heterogeneous populations. SPOTlight relies on imaging visual phenotypes by microscopy, precise optical tagging of single target cells, and retrieval of tagged cells by fluorescence-activated cell sorting. To illustrate SPOTlight's ability to screen cells based on temporal properties, we chose to develop a photostable yellow fluorescent protein for extended imaging experiments. We screened 3 million cells expressing mutagenesis libraries and identified a bright new variant, mGold, that is the most photostable yellow fluorescent protein reported to date. We anticipate that the versatility of SPOTlight will facilitate its deployment to decipher the rules of life, understand diseases, and engineer new molecules and cells.
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Affiliation(s)
- Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Peter H Suzuki
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - John F Ahrens
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Sihui Guan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Olombrada M, Peña C, Rodríguez-Galán O, Klingauf-Nerurkar P, Portugal-Calisto D, Oborská-Oplová M, Altvater M, Gavilanes JG, Martínez-Del-Pozo Á, de la Cruz J, García-Ortega L, Panse VG. The ribotoxin α-sarcin can cleave the sarcin/ricin loop on late 60S pre-ribosomes. Nucleic Acids Res 2020; 48:6210-6222. [PMID: 32365182 PMCID: PMC7293039 DOI: 10.1093/nar/gkaa315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/27/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
The ribotoxin α-sarcin belongs to a family of ribonucleases that cleave the sarcin/ricin loop (SRL), a critical functional rRNA element within the large ribosomal subunit (60S), thereby abolishing translation. Whether α-sarcin targets the SRL only in mature 60S subunits remains unresolved. Here, we show that, in yeast, α-sarcin can cleave SRLs within late 60S pre-ribosomes containing mature 25S rRNA but not nucleolar/nuclear 60S pre-ribosomes containing 27S pre-rRNA in vivo. Conditional expression of α-sarcin is lethal, but does not impede early pre-rRNA processing, nuclear export and the cytoplasmic maturation of 60S pre-ribosomes. Thus, SRL-cleaved containing late 60S pre-ribosomes seem to escape cytoplasmic proofreading steps. Polysome analyses revealed that SRL-cleaved 60S ribosomal subunits form 80S initiation complexes, but fail to progress to the step of translation elongation. We suggest that the functional integrity of a α-sarcin cleaved SRL might be assessed only during translation.
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Affiliation(s)
- Miriam Olombrada
- Departamento de Bioquímica y Biología Molecular, Facultad de Química, Universidad Complutense de Madrid, Spain.,Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, CH-8093 Zürich, Switzerland
| | - Cohue Peña
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, CH-8093 Zürich, Switzerland.,Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, CH-8006 Zürich, Switzerland
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Purnima Klingauf-Nerurkar
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, CH-8093 Zürich, Switzerland.,Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, CH-8006 Zürich, Switzerland
| | - Daniela Portugal-Calisto
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, CH-8006 Zürich, Switzerland
| | - Michaela Oborská-Oplová
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, CH-8093 Zürich, Switzerland.,Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, CH-8006 Zürich, Switzerland
| | - Martin Altvater
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, CH-8093 Zürich, Switzerland
| | - José G Gavilanes
- Departamento de Bioquímica y Biología Molecular, Facultad de Química, Universidad Complutense de Madrid, Spain
| | - Álvaro Martínez-Del-Pozo
- Departamento de Bioquímica y Biología Molecular, Facultad de Química, Universidad Complutense de Madrid, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Lucía García-Ortega
- Departamento de Bioquímica y Biología Molecular, Facultad de Química, Universidad Complutense de Madrid, Spain
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zürich, Gloriastrasse 30, CH-8006 Zürich, Switzerland
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22
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Nakano S, Konishi H, Morii T. Receptor-based fluorescent sensors constructed from ribonucleopeptide. Methods Enzymol 2020; 641:183-223. [PMID: 32713523 DOI: 10.1016/bs.mie.2020.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Receptor-based fluorescent sensors are the representative tool for quantitative detection of target ligands. The high substrate-selectivity originated from biomacromolecule receptor is one of the advantages of this tool, but a laborious trial and error is usually required to construct sensors showing satisfactory fluorescence intensity changes without diminishing the function of parent receptor. Ribonucleopeptide (RNP) provides a scaffold of fluorescent sensors to improve such issues. RNP receptors for the ligand of interest are constructed by applying in vitro selection for RNA-derived RNP library. Simple modification of the N-terminal of peptide in RNP by an appropriate fluorophore converts the RNP receptor into the fluorescent sensor with retaining the affinity and selectivity for the substrate. In this chapter, we introduce the protocols for construction of fluorescent RNP sensors through selection from a library of fluorophore-modified RNP complex or by a structure-based modular design. Furthermore, we describe the application of covalently linked RNP sensors for simultaneous detection of multiple ligands.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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23
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Recovery and Reusability of ApoUnaG Fluorescence Protein from the Unconjugated Bilirubin Complex Structure. J Fluoresc 2020; 30:497-503. [DOI: 10.1007/s10895-020-02519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/14/2020] [Indexed: 10/24/2022]
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24
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Zhou JG, Yang S, Deng ZY, Leszczynski J. Relative Order of Acidity among Hydroxyl Groups of Oxyluciferin and Emission Light Colors in Aqueous Solution. J Photochem Photobiol A Chem 2020; 397. [PMID: 32612342 DOI: 10.1016/j.jphotochem.2020.112504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The magnitude of the acidity of the oxyluciferin in water in the ground and excited state is investigated, and it is found for the first time using computational approach that the enol group of the phenol-enol species is the most acidic in the ground state, but the deprotonation of the phenol of the phenol-keto form is the most favored in the excited state. The relative order of the acidity among the hydroxyl groups in the oxyluciferin is attributed to the sequence of the O-H bond lengths in the enol and phenol group of the phenol-enol form, and the phenol group of the phenol-keto species. The mechanism of determining the dominant emissive species in the excited state is proposed, and the dependence of emission light colors on the photoexcitation energy is elucidated by the high relative concentration of six chemical forms in the ground state and the absorption efficiency.
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Affiliation(s)
- Jian-Ge Zhou
- Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi 39217, United States.,Department of Chemistry, Physics and Atmospheric Science, Jackson State University, Jackson, Mississippi 39217, United States
| | - Shan Yang
- Department of Chemistry, Physics and Atmospheric Science, Jackson State University, Jackson, Mississippi 39217, United States
| | - Zhen-Yan Deng
- Department of Physics, Shanghai University, Shanghai 200444, China
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi 39217, United States.,Department of Chemistry, Physics and Atmospheric Science, Jackson State University, Jackson, Mississippi 39217, United States
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25
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Santos EM, Berbasova T, Wang W, Salmani RE, Sheng W, Vasileiou C, Geiger JH, Borhan B. Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging. Chembiochem 2020; 21:723-729. [PMID: 31482666 PMCID: PMC7379159 DOI: 10.1002/cbic.201900428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 12/25/2022]
Abstract
A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.
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Affiliation(s)
- Elizabeth M. Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Wenjing Wang
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | | | - Wei Sheng
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
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26
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Howell AH, Peters WS, Knoblauch M. The diffusive injection micropipette (DIMP). JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153060. [PMID: 31765880 DOI: 10.1016/j.jplph.2019.153060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2023]
Abstract
The microinjection of fluorescent probes into live cells is an essential component in the toolbox of modern cell biology. Microinjection techniques include the penetration of the plasma membrane and, if present, the cell wall with micropipettes, and the application of pressure or electrical currents to drive the micropipette contents into the cell. These procedures interfere with cellular functions and therefore may induce artifacts. We designed the diffusive injection micropipette (DIMP) that avoids most of the possible artifacts due to the drastically reduced volume of its fluid contents and the utilization of diffusion for cargo delivery into the target cell. DIMPs were successfully tested in plant, fungal, and animal cells. Using the continuity of cytoplasmic dynamics over ten minutes after impalement of Nicotiana trichome cells as a criterion for non-invasiveness, we found DIMPs significantly less disruptive than conventional pressure microinjection. The design of DIMPs abolishes major sources of artifacts that cannot be avoided by other microinjection techniques. Moreover, DIMPs are inexpensive, easy to produce, and can be applied without specific equipment other than a micromanipulator. With these features, DIMPs may become the tool of choice for studies that require the least invasive delivery possible of materials into live cells.
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Affiliation(s)
- Alexander H Howell
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Winfried S Peters
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
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27
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Deng H, Yan S, Huang Y, Lei C, Nie Z. Design strategies for fluorescent proteins/mimics and their applications in biosensing and bioimaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Bollinger A, Thies S, Katzke N, Jaeger K. The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena. Microb Biotechnol 2020; 13:19-31. [PMID: 29943398 PMCID: PMC6922532 DOI: 10.1111/1751-7915.13288] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Nadine Katzke
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHD‐52425JülichGermany
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29
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Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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30
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FÖrster resonance energy transfer (FRET)-based biosensors for biological applications. Biosens Bioelectron 2019; 138:111314. [DOI: 10.1016/j.bios.2019.05.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022]
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31
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Rhodopsin-based voltage imaging tools for use in muscles and neurons of Caenorhabditis elegans. Proc Natl Acad Sci U S A 2019; 116:17051-17060. [PMID: 31371514 PMCID: PMC6708366 DOI: 10.1073/pnas.1902443116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neuronal and other excitable cell activity is characterized by alteration in membrane voltage, while intracellular Ca2+ levels and transmitter release are affected downstream of electrical activity. Thus, the most direct way of monitoring neuronal activity is by membrane voltage. Electrophysiology is demanding for multiple cells or cell ensembles and difficult to use in live animals, thus imaging methods are desirable. Yet, genetically encoded voltage indicators fell behind Ca2+ indicators until recently, when microbial rhodopsins and derivatives were introduced as genetically encoded voltage indicators. We evaluated rhodopsin tools for voltage imaging in muscles and neurons of Caenorhabditis elegans, a prime animal model in neuro- and cell biology, showing robust performance and the ability to characterize genetic mutants. Genetically encoded voltage indicators (GEVIs) based on microbial rhodopsins utilize the voltage-sensitive fluorescence of all-trans retinal (ATR), while in electrochromic FRET (eFRET) sensors, donor fluorescence drops when the rhodopsin acts as depolarization-sensitive acceptor. In recent years, such tools have become widely used in mammalian cells but are less commonly used in invertebrate systems, mostly due to low fluorescence yields. We systematically assessed Arch(D95N), Archon, QuasAr, and the eFRET sensors MacQ-mCitrine and QuasAr-mOrange, in the nematode Caenorhabditis elegans. ATR-bearing rhodopsins reported on voltage changes in body wall muscles (BWMs), in the pharynx, the feeding organ [where Arch(D95N) showed approximately 128% ΔF/F increase per 100 mV], and in neurons, integrating circuit activity. ATR fluorescence is very dim, yet, using the retinal analog dimethylaminoretinal, it was boosted 250-fold. eFRET sensors provided sensitivities of 45 to 78% ΔF/F per 100 mV, induced by BWM action potentials, and in pharyngeal muscle, measured in simultaneous optical and sharp electrode recordings, MacQ-mCitrine showed approximately 20% ΔF/F per 100 mV. All sensors reported differences in muscle depolarization induced by a voltage-gated Ca2+-channel mutant. Optogenetically evoked de- or hyperpolarization of motor neurons increased or eliminated action potential activity and caused a rise or drop in BWM sensor fluorescence. Finally, we analyzed voltage dynamics across the entire pharynx, showing uniform depolarization but compartmentalized repolarization of anterior and posterior parts. Our work establishes all-optical, noninvasive electrophysiology in live, intact C. elegans.
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32
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Otero C, Carreño A, Polanco R, Llancalahuen FM, Arratia-Pérez R, Gacitúa M, Fuentes JA. Rhenium (I) Complexes as Probes for Prokaryotic and Fungal Cells by Fluorescence Microscopy: Do Ligands Matter? Front Chem 2019; 7:454. [PMID: 31297366 PMCID: PMC6606945 DOI: 10.3389/fchem.2019.00454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/07/2019] [Indexed: 12/22/2022] Open
Abstract
Re(I) complexes have exposed highly suitable properties for cellular imaging (especially for fluorescent microscopy) such as low cytotoxicity, good cellular uptake, and differential staining. These features can be modulated or tuned by modifying the ligands surrounding the metal core. However, most of Re(I)-based complexes have been tested for non-walled cells, such as epithelial cells. In this context, it has been proposed that Re(I) complexes are inefficient to stain walled cells (i.e., cells protected by a rigid cell wall, such as bacteria and fungi), presumably due to this physical barrier hampering cellular uptake. More recently, a series of studies have been published showing that a suitable combination of ligands is useful for obtaining Re(I)-based complexes able to stain walled cells. This review summarizes the main characteristics of different fluorophores used in bioimage, remarking the advantages of d6-based complexes, and focusing on Re(I) complexes. In addition, we explored different structural features of these complexes that allow for obtaining fluorophores especially designed for walled cells (bacteria and fungi), with especial emphasis on the ligand choice. Since many pathogens correspond to bacteria and fungi (yeasts and molds), and considering that these organisms have been increasingly used in several biotechnological applications, development of new tools for their study, such as the design of new fluorophores, is fundamental and attractive.
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Affiliation(s)
- Carolina Otero
- Facultad de Medicina, Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Alexander Carreño
- Center for Applied Nanosciences (CANS), Universidad Andres Bello, Santiago, Chile
| | - Rubén Polanco
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago, Chile
| | - Felipe M Llancalahuen
- Facultad de Medicina, Escuela de Química y Farmacia, Universidad Andres Bello, Santiago, Chile
| | - Ramiro Arratia-Pérez
- Center for Applied Nanosciences (CANS), Universidad Andres Bello, Santiago, Chile
| | - Manuel Gacitúa
- Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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33
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Nakano S, Shimizu M, Dinh H, Morii T. Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors. Chem Commun (Camb) 2019; 55:1611-1614. [PMID: 30657140 DOI: 10.1039/c8cc09934k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold. These sensors allow facile and quantitative detection of ATP and ADP simultaneously in a solution and enable monitoring of the time-course changes of ATP and ADP concentrations in an enzymatic reaction.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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34
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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35
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The power of combining phenotypic and target-focused drug discovery. Drug Discov Today 2019; 24:526-532. [DOI: 10.1016/j.drudis.2018.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
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36
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Kim SE, Hwang KY, Nam KH. Spectral and structural analysis of a red fluorescent protein from Acropora digitifera. Protein Sci 2019; 28:375-381. [PMID: 30368951 PMCID: PMC6319757 DOI: 10.1002/pro.3540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Fluorescent proteins (FPs) possess a wide variety of spectral properties that make them of widespread interest as optical markers. These proteins can be applied as pH indicators or metal biosensors. The discovery and characterization of new fluorescent proteins is expected to further extend their application. Here, we report the spectral and structural analysis of a red fluorescent protein from Acropora digitifera (designated AdRed). This protein shows a tetrameric state and is red emitting, with excitation and emission maxima at 567 and 612 nm, respectively. Its crystal structure shows the tetrameric interface stabilized by hydrogen bonding and salt bridges. The electron density map of the chromophore, consisting of Asp66-Tyr67-Gly68, shows the decarboxylated side chain of Asp66. Ser223, located near the chromophore, has the role of bridging His202 and Glu221, and is part of the hydrogen bond network. Mutated AdRed with Cys148Ser reveals a blue shift in fluorescence excitation and emission. Our results provide insights into understanding the molecular function of AdRed and other FPs.
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Affiliation(s)
- So Eun Kim
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
- Institute of Life Science and Natural ResourcesKorea UniversitySeoul02841Republic of Korea
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37
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Wang L, Chen X, Guo X, Li J, Liu Q, Kang F, Wang X, Hu C, Liu H, Gong W, Zhuang W, Liu X, Wang J. Significant expansion and red-shifting of fluorescent protein chromophore determined through computational design and genetic code expansion. BIOPHYSICS REPORTS 2018; 4:273-285. [PMID: 30533492 PMCID: PMC6245237 DOI: 10.1007/s41048-018-0073-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/17/2018] [Indexed: 11/11/2022] Open
Abstract
ABSTRACT Fluorescent proteins (FPs) with emission wavelengths in the far-red and infrared regions of the spectrum provide powerful tools for deep-tissue and super-resolution imaging. The development of red-shifted FPs has evoked widespread interest and continuous engineering efforts. In this article, based on a computational design and genetic code expansion, we report a rational approach to significantly expand and red-shift the chromophore of green fluorescent protein (GFP). We applied computational calculations to predict the excitation and emission wavelengths of a FP chromophore harboring unnatural amino acids (UAA) and identify in silico an appropriate UAA, 2-amino-3-(6-hydroxynaphthalen-2-yl)propanoic acid (naphthol-Ala). Our methodology allowed us to formulate a GFP variant (cpsfGFP-66-Naphthol-Ala) with red-shifted absorbance and emission spectral maxima exceeding 60 and 130 nm, respectively, compared to those of GFP. The GFP chromophore is formed through autocatalytic post-translational modification to generate a planar 4-(p-hydroxybenzylidene)-5-imidazolinone chromophore. We solved the crystal structure of cpsfGFP-66-naphthol-Ala at 1.3 Å resolution and demonstrated the formation of a much larger conjugated π-system when the phenol group is replaced by naphthol. These results explain the significant red-shifting of the excitation and emission spectra of cpsfGFP-66-naphthol-Ala. GRAPHICAL ABSTRACT
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Affiliation(s)
- Li Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University, Changchun, 130012 China
| | - Xuzhen Guo
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiasong Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qi Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fuying Kang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xudong Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Cheng Hu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Haiping Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Weimin Gong
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002 China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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38
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Genetically encoded fluorescent indicators for live cell pH imaging. Biochim Biophys Acta Gen Subj 2018; 1862:2924-2939. [PMID: 30279147 DOI: 10.1016/j.bbagen.2018.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intracellular pH underlies most cellular processes. There is emerging evidence of a pH-signaling role in plant cells and microorganisms. Dysregulation of pH is associated with human diseases, such as cancer and Alzheimer's disease. SCOPE OF REVIEW In this review, we attempt to provide a summary of the progress that has been made in the field during the past two decades. First, we present an overview of the current state of the design and applications of fluorescent protein (FP)-based pH indicators. Then, we turn our attention to the development and applications of hybrid pH sensors that combine the capabilities of non-GFP fluorophores with the advantages of genetically encoded tags. Finally, we discuss recent advances in multicolor pH imaging and the applications of genetically encoded pH sensors in multiparameter imaging. MAJOR CONCLUSIONS Genetically encoded pH sensors have proven to be indispensable noninvasive tools for selective targeting to different cellular locations. Although a variety of genetically encoded pH sensors have been designed and applied at the single cell level, there is still much room for improvements and future developments of novel powerful tools for pH imaging. Among the most pressing challenges in this area is the design of brighter redshifted sensors for tissue research and whole animal experiments. GENERAL SIGNIFICANCE The design of precise pH measuring instruments is one of the important goals in cell biochemistry and may give rise to the development of new powerful diagnostic tools for various diseases.
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Sano T, Kobayashi T, Ogawa O, Matsuda M. Gliding Basal Cell Migration of the Urothelium during Wound Healing. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:2564-2573. [PMID: 30121259 DOI: 10.1016/j.ajpath.2018.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/01/2018] [Accepted: 07/02/2018] [Indexed: 01/04/2023]
Abstract
Collective cell migration during wound healing has been extensively studied in the epidermis. However, it remains unknown whether the urothelium repairs wounds in a manner similar to the epidermis. By in vivo two-photon excitation microscopy of transgenic mice that express fluorescent biosensors, we studied the collective cell migration of the urothelium in comparison with that of the epidermis. In vivo time-lapse imaging revealed that, even in the absence of a wound, urothelial cells continuously moved and sometimes glided as a sheet over the underlying lamina propria. On abrasion of the epithelium, the migration speed of each epidermal cell was inversely correlated with the distance to the wound edge. Repetitive activation waves of extracellular signal-regulated kinase (ERK) were generated at and propagated away from the wound edge. In contrast, urothelial cells glided as a sheet over the lamina propria without any ERK activation waves. Accordingly, the mitogen-activated protein kinase/ERK kinase inhibitor PD0325901 decreased the migration velocity of the epidermis but not the urothelium. Interestingly, the tyrosine kinase inhibitor dasatinib inhibited migration of the urothelium as well as the epidermis, suggesting that the gliding migration of the urothelium is an active, not a passive, migration. In conclusion, the urothelium glides over the lamina propria to fill wounds in an ERK-independent manner, whereas the epidermis crawls to cover wounds in an ERK-dependent manner.
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Affiliation(s)
- Takeshi Sano
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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40
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Yoon S, Rossi JJ. Targeted Molecular Imaging Using Aptamers in Cancer. Pharmaceuticals (Basel) 2018; 11:ph11030071. [PMID: 30029472 PMCID: PMC6160950 DOI: 10.3390/ph11030071] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 12/21/2022] Open
Abstract
Imaging is not only seeing, but also believing. For targeted imaging modalities, nucleic acid aptamers have features such as superior recognition of structural epitopes and quick uptake in target cells. This explains the emergence of an evolved new class of aptamers into a wide spectrum of imaging applications over the last decade. Genetically encoded biosensors tagged with fluorescent RNA aptamers have been developed as intracellular imaging tools to understand cellular signaling and physiology in live cells. Cancer-specific aptamers labeled with fluorescence have been used for assessment of clinical tissue specimens. Aptamers conjugated with gold nanoparticles have been employed to develop innovative mass spectrometry tissue imaging. Also, use of chemically conjugated cancer-specific aptamers as probes for non-invasive and high-resolution imaging has been transformative for in vivo imaging in multiple cancers.
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Affiliation(s)
- Sorah Yoon
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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41
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A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging. Sci Rep 2018; 8:8984. [PMID: 29895862 PMCID: PMC5997707 DOI: 10.1038/s41598-018-27174-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/25/2018] [Indexed: 02/04/2023] Open
Abstract
Genetically encoded biosensors based on the principle of Förster resonance energy transfer comprise two major classes: biosensors based on fluorescence resonance energy transfer (FRET) and those based on bioluminescence energy transfer (BRET). The FRET biosensors visualize signaling-molecule activity in cells or tissues with high resolution. Meanwhile, due to the low background signal, the BRET biosensors are primarily used in drug screening. Here, we report a protocol to transform intramolecular FRET biosensors to BRET-FRET hybrid biosensors called hyBRET biosensors. The hyBRET biosensors retain all properties of the prototype FRET biosensors and also work as BRET biosensors with dynamic ranges comparable to the prototype FRET biosensors. The hyBRET biosensors are compatible with optogenetics, luminescence microplate reader assays, and non-invasive whole-body imaging of xenograft and transgenic mice. This simple protocol will expand the use of FRET biosensors and enable visualization of the multiscale dynamics of cell signaling in live animals.
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42
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Bae Y, Kim GJ, Kim H, Park SG, Jung HS, Kang S. Engineering Tunable Dual Functional Protein Cage Nanoparticles Using Bacterial Superglue. Biomacromolecules 2018; 19:2896-2904. [DOI: 10.1021/acs.biomac.8b00457] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yoonji Bae
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Gwang Joong Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do 24341, Korea
| | - Hansol Kim
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Seong Guk Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do 24341, Korea
| | - Sebyung Kang
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
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43
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Zhang Q, Zhang J, Gavathiotis E. ICBS 2017 in Shanghai-Illuminating Life with Chemical Innovation. ACS Chem Biol 2018; 13:1111-1122. [PMID: 29677443 PMCID: PMC6855916 DOI: 10.1021/acschembio.8b00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Evripidis Gavathiotis
- Department of Biochemistry, Department of Medicine, Albert Einstein College of Medicine, New York 10461, United States
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44
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Abstract
Immunofluorescence microscopy is an invaluable tool for the study of biological processes at the cellular level. While the localization of surface-exposed antigens can easily be determined using fluorescent antibodies, localization of intracellular antigens requires permeabilization of the bacterial cell wall and membrane. Here, we describe an immunofluorescence protocol tailored specifically for Streptococcus pyogenes, applying the phage lysin PlyC for cell wall permeabilization. This protocol allows a high level of morphological preservation, suitable for high-resolution microscopy. With slight modification, this protocol could also be used for other Gram-positive pathogens.
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45
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Zaki AJ, Hartley A, Reddington SC, Thomas SK, Watson P, Hayes A, Moskalenko AV, Craciun MF, Macdonald JE, Jones DD, Elliott M. Defined covalent assembly of protein molecules on graphene using a genetically encoded photochemical reaction handle. RSC Adv 2018; 8:5768-5775. [PMID: 35539607 PMCID: PMC9078156 DOI: 10.1039/c7ra11166e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/11/2018] [Indexed: 11/27/2022] Open
Abstract
We have created modified protein variants by introducing a non-canonical amino acid p-azido-l-phenylalanine (azF) into defined positions for photochemically-induced covalent attachment to graphene. Attachment of GFP, TEM and cyt b562 proteins was verified through a combination of atomic force and scanning tunnelling microscopy, resistance measurements, Raman data and fluorescence measurements. This method can in principle be extended to any protein which can be engineered in this way without adversely affecting its structural stability. We demonstrate a general method for photochemically-induced covalent attachment of proteins to graphene through the introduction of a non-canonical amino acid p-azido-l-phenylalanine into defined residue positions.![]()
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Affiliation(s)
- Athraa J. Zaki
- School of Physics and Astronomy
- Cardiff University
- Cardiff CF24 3AA
- UK
| | | | | | | | | | | | | | | | | | | | - Martin Elliott
- School of Physics and Astronomy
- Cardiff University
- Cardiff CF24 3AA
- UK
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46
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Cytotoxicity Test Based on Human Cells Labeled with Fluorescent Proteins: Fluorimetry, Photography, and Scanning for High-Throughput Assay. Mol Imaging Biol 2017; 20:368-377. [DOI: 10.1007/s11307-017-1152-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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47
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Delbeke J, Hoffman L, Mols K, Braeken D, Prodanov D. And Then There Was Light: Perspectives of Optogenetics for Deep Brain Stimulation and Neuromodulation. Front Neurosci 2017; 11:663. [PMID: 29311765 PMCID: PMC5732983 DOI: 10.3389/fnins.2017.00663] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Deep Brain Stimulation (DBS) has evolved into a well-accepted add-on treatment for patients with severe Parkinsons disease as well as for other chronic neurological conditions. The focal action of electrical stimulation can yield better responses and it exposes the patient to fewer side effects compared to pharmaceuticals distributed throughout the body toward the brain. On the other hand, the current practice of DBS is hampered by the relatively coarse level of neuromodulation achieved. Optogenetics, in contrast, offers the perspective of much more selective actions on the various physiological structures, provided that the stimulated cells are rendered sensitive to the action of light. Optogenetics has experienced tremendous progress since its first in vivo applications about 10 years ago. Recent advancements of viral vector technology for gene transfer substantially reduce vector-associated cytotoxicity and immune responses. This brings about the possibility to transfer this technology into the clinic as a possible alternative to DBS and neuromodulation. New paths could be opened toward a rich panel of clinical applications. Some technical issues still limit the long term use in humans but realistic perspectives quickly emerge. Despite a rapid accumulation of observations about patho-physiological mechanisms, it is still mostly serendipity and empiric adjustments that dictate clinical practice while more efficient logically designed interventions remain rather exceptional. Interestingly, it is also very much the neuro technology developed around optogenetics that offers the most promising tools to fill in the existing knowledge gaps about brain function in health and disease. The present review examines Parkinson's disease and refractory epilepsy as use cases for possible optogenetic stimulation therapies.
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Affiliation(s)
- Jean Delbeke
- LCEN3, Department of Neurology, Institute of Neuroscience, Ghent University, Ghent, Belgium
| | | | - Katrien Mols
- Neuroscience Research Flanders, Leuven, Belgium.,Life Science and Imaging, Imec, Leuven, Belgium
| | | | - Dimiter Prodanov
- Neuroscience Research Flanders, Leuven, Belgium.,Environment, Health and Safety, Imec, Leuven, Belgium
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48
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Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M. Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI. RNA (NEW YORK, N.Y.) 2017; 23:1788-1795. [PMID: 28939697 PMCID: PMC5689000 DOI: 10.1261/rna.063008.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 09/05/2017] [Indexed: 05/05/2023]
Abstract
Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach, comprising five mutations for which the exact role has not yet been deciphered. In this work, we cocrystallized a reengineered version of iSpinach in complex with the DFHBI and solved the X-ray structure of the complex at 2 Å resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach sheds some light on the possible function of the different beneficial mutations carried by iSpinach.
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Affiliation(s)
- Pablo Fernandez-Millan
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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49
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Khrenova MG, Meteleshko YI, Nemukhin AV. Mutants of the Flavoprotein iLOV as Prospective Red-Shifted Fluorescent Markers. J Phys Chem B 2017; 121:10018-10025. [DOI: 10.1021/acs.jpcb.7b07533] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia I. Meteleshko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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50
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Nakano S, Tamura T, Das RK, Nakata E, Chang YT, Morii T. A Diversity-Oriented Library of Fluorophore-Modified Receptors Constructed from a Chemical Library of Synthetic Fluorophores. Chembiochem 2017; 18:2212-2216. [PMID: 28879678 DOI: 10.1002/cbic.201700403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/16/2022]
Abstract
The practical application of biosensors can be determined by evaluating the sensing ability of fluorophore-modified derivatives of a receptor with appropriate recognition characteristics for target molecules. One of the key determinants for successfully obtaining a useful biosensor is wide variation in the fluorophores attached to a given receptor. Thus, using a larger fluorophore-modified receptor library provides a higher probability of obtaining a practically useful biosensor. However, no effective method has yet been developed for constructing such a diverse library of fluorophore-modified receptors. Herein, we report a method for constructing fluorophore-modified receptors by using a chemical library of synthetic fluorophores with a thiol-reactive group. This library was converted into a library of fluorophore-modified adenosine-binding ribonucleopeptide (RNP) receptors by introducing the fluorophores to the Rev peptide of the RNP complex by alkylation of the thiol group. This method enabled the construction of 263 fluorophore-modified ATP-binding RNP receptors and allowed the selection of suitable receptor-based fluorescent sensors that target ATP.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Raj Kumar Das
- Bharat Petroleum Corporation Ltd., Corporate R&D Centre, Plot No. 2 A, Udyog Kendra, Surajpur Industrial Area, Greater Noida, 201 306, India
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Young-Tae Chang
- Department of Chemistry and MedChem Program of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
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