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Chen J, Huang Z, Xiao J, Du S, Bu Q, Guo H, Ye J, Chen S, Gao J, Li Z, Lan M, Wang S, Zhang T, Zhang J, Wu Y, Zhang Y, Xia N, Yuan Q, Cheng T. A quadri-fluorescence SARS-CoV-2 pseudovirus system for efficient antigenic characterization of multiple circulating variants. CELL REPORTS METHODS 2024; 4:100856. [PMID: 39243752 PMCID: PMC11440059 DOI: 10.1016/j.crmeth.2024.100856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/18/2024] [Accepted: 08/14/2024] [Indexed: 09/09/2024]
Abstract
The ongoing co-circulation of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains necessitates advanced methods such as high-throughput multiplex pseudovirus systems for evaluating immune responses to different variants, crucial for developing updated vaccines and neutralizing antibodies (nAbs). We have developed a quadri-fluorescence (qFluo) pseudovirus platform by four fluorescent reporters with different spectra, allowing simultaneous measurement of the nAbs against four variants in a single test. qFluo shows high concordance with the classical single-reporter assay when testing monoclonal antibodies and human plasma. Utilizing qFluo, we assessed the immunogenicities of the spike of BA.5, BQ.1.1, XBB.1.5, and CH.1.1 in hamsters. An analysis of cross-neutralization against 51 variants demonstrated superior protective immunity from XBB.1.5, especially against prevalent strains such as "FLip" and JN.1, compared to BA.5. Our finding partially fills the knowledge gap concerning the immunogenic efficacy of the XBB.1.5 vaccine against current dominant variants, being instrumental in vaccine-strain decisions and insight into the evolutionary path of SARS-CoV-2.
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Affiliation(s)
- Jijing Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Jin Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Shuangling Du
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Qingfang Bu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Huilin Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Jianghui Ye
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Shiqi Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jiahua Gao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Zonglin Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Miaolin Lan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Shaojuan Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Tianying Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Shanghai Institute of Infectious Diseases and Biosecurity, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Yangtao Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China.
| | - Yali Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China.
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China
| | - Quan Yuan
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China.
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, P.R. China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, P.R. China.
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2
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Nam KH, Xu Y. Structural Analysis of the Large Stokes Shift Red Fluorescent Protein tKeima. Molecules 2024; 29:2579. [PMID: 38893454 PMCID: PMC11173989 DOI: 10.3390/molecules29112579] [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: 04/25/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The Keima family comprises large Stokes shift fluorescent proteins that are useful for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. The tKeima is a tetrameric large Stokes shift fluorescent protein and serves as the ancestor fluorescent protein for both dKeima and mKeima. The spectroscopic properties of tKeima have been previously reported; however, its structural basis and molecular properties have not yet been elucidated. In this study, we present the crystallographic results of the large Stokes shift fluorescent protein tKeima. The purified tKeima protein spontaneously crystallized after purification without further crystallization. The crystal structure of tKeima was determined at 3.0 Å resolution, revealing a β-barrel fold containing the Gln-Tyr-Gly chromophores mainly with cis-conformation. The tetrameric interfaces of tKeima were stabilized by numerous hydrogen bonds and salt-bridge interactions. These key residues distinguish the substituted residues in dKeima and mKeima. The key structure-based residues involved in the tetramer formation of tKeima provide insights into the generation of a new type of monomeric mKeima. This structural analysis expands our knowledge of the Keima family and provides insights into its protein engineering.
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Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China
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3
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Hu J, Yang F, Liu C, Wang N, Xiao Y, Zhai Y, Wang X, Zhang R, Gao L, Xu M, Wang J, Liu Z, Huang S, Liu W, Hu Y, Liu F, Guo Y, Wang L, Yuan J, Zhang Z, Chu J. UFObow: A single-wavelength excitable Brainbow for simultaneous multicolor ex-vivo and in-vivo imaging of mammalian cells. Commun Biol 2024; 7:394. [PMID: 38561421 PMCID: PMC10984974 DOI: 10.1038/s42003-024-06062-3] [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: 06/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Brainbow is a genetic cell-labeling technique that allows random colorization of multiple cells and real-time visualization of cell fate within a tissue, providing valuable insights into understanding complex biological processes. However, fluorescent proteins (FPs) in Brainbow have distinct excitation spectra with peak difference greater than 35 nm, which requires sequential imaging under multiple excitations and thus leads to long acquisition times. In addition, they are not easily used together with other fluorophores due to severe spectral bleed-through. Here, we report the development of a single-wavelength excitable Brainbow, UFObow, incorporating three newly developed blue-excitable FPs. We have demonstrated that UFObow enables not only tracking the growth dynamics of tumor cells in vivo but also mapping spatial distribution of immune cells within a sub-cubic centimeter tissue, revealing cell heterogeneity. This provides a powerful means to explore complex biology in a simultaneous imaging manner at a single-cell resolution in organs or in vivo.
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Affiliation(s)
- Jiahong Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fangfang Yang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chong Liu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Nengzhi Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yinghan Xiao
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yujie Zhai
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xinru Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ren Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Lulu Gao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Mengli Xu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Jialu Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zheng Liu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Songlin Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China
| | - Wenfeng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yajing Hu
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Feng Liu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liang Wang
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jing Yuan
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Zhihong Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, Hainan, 570228, China.
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology & CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen, 518055, 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: 15] [Impact Index Per Article: 15.0] [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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Mao M, Qian Y, Zhang W, Zhou S, Wang Z, Chen X, Yang Y. Controlling protein stability with SULI, a highly sensitive tag for stabilization upon light induction. Nat Commun 2023; 14:2172. [PMID: 37061509 PMCID: PMC10105765 DOI: 10.1038/s41467-023-37830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Optogenetics tools for precise temporal and spatial control of protein abundance are valuable in studying diverse complex biological processes. In the present study, we engineer a monomeric tag of stabilization upon light induction (SULI) for yeast and zebrafish based on a single light-oxygen-voltage domain from Neurospora crassa. Proteins of interest fused with SULI are stable upon light illumination but are readily degraded after transfer to dark conditions. SULI shows a high dynamic range and a high tolerance to fusion at different positions of the target protein. Further studies reveal that SULI-mediated degradation occurs through a lysine ubiquitination-independent proteasome pathway. We demonstrate the usefulness of SULI in controlling the cell cycle in yeast and regulating protein stability in zebrafish, respectively. Overall, our data indicate that SULI is a simple and robust tool to quantitatively and spatiotemporally modulate protein levels for biotechnological or biomedical applications.
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Affiliation(s)
- Miaowei Mao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajie Qian
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Wenyao Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Siyu Zhou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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7
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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8
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Peng W, Maydew CC, Kam H, Lynd JK, Tutol JN, Phelps SM, Abeyrathna S, Meloni G, Dodani SC. Discovery of a monomeric green fluorescent protein sensor for chloride by structure-guided bioinformatics. Chem Sci 2022; 13:12659-12672. [PMID: 36519056 PMCID: PMC9645410 DOI: 10.1039/d2sc03903f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Chloride is an essential anion for all forms of life. Beyond electrolyte balance, an increasing body of evidence points to new roles for chloride in normal physiology and disease. Over the last two decades, this understanding has been advanced by chloride-sensitive fluorescent proteins for imaging applications in living cells. To our surprise, these sensors have primarily been engineered from the green fluorescent protein (GFP) found in the jellyfish Aequorea victoria. However, the GFP family has a rich sequence space that could already encode for new sensors with desired properties, thereby minimizing protein engineering efforts and accelerating biological applications. To efficiently sample this space, we present and validate a stepwise bioinformatics strategy focused first on the chloride binding pocket and second on a monomeric oligomerization state. Using this, we identified GFPxm163 from GFPxm found in the jellyfish Aequorea macrodactyla. In vitro characterization shows that the binding of chloride as well as bromide, iodide, and nitrate rapidly tunes the ground state chromophore equilibrium from the phenolate to the phenol state generating a pH-dependent, turn-off fluorescence response. Furthermore, live-cell fluorescence microscopy reveals that GFPxm163 provides a reversible, yet indirect readout of chloride transport via iodide exchange. With this demonstration, we anticipate that the pairing of bioinformatics with protein engineering methods will provide an efficient methodology to discover and design new chloride-sensitive fluorescent proteins for cellular applications.
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Affiliation(s)
- Weicheng Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
- Department of Biological Sciences, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Caden C Maydew
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Hiu Kam
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Jacob K Lynd
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Jasmine N Tutol
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Shelby M Phelps
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Sameera Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson 75080 Texas USA
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9
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Leben R, Lindquist RL, Hauser AE, Niesner R, Rakhymzhan A. Two-Photon Excitation Spectra of Various Fluorescent Proteins within a Broad Excitation Range. Int J Mol Sci 2022; 23:13407. [PMID: 36362194 PMCID: PMC9656010 DOI: 10.3390/ijms232113407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 03/26/2024] Open
Abstract
Two-photon excitation fluorescence laser-scanning microscopy is the preferred method for studying dynamic processes in living organ models or even in living organisms. Thanks to near-infrared and infrared excitation, it is possible to penetrate deep into the tissue, reaching areas of interest relevant to life sciences and biomedicine. In those imaging experiments, two-photon excitation spectra are needed to select the optimal laser wavelength to excite as many fluorophores as possible simultaneously in the sample under consideration. The more fluorophores that can be excited, and the more cell populations that can be studied, the better access to their arrangement and interaction can be reached in complex systems such as immunological organs. However, for many fluorophores, the two-photon excitation properties are poorly predicted from the single-photon spectra and are not yet available, in the literature or databases. Here, we present the broad excitation range (760 nm to 1300 nm) of photon-flux-normalized two-photon spectra of several fluorescent proteins in their cellular environment. This includes the following fluorescent proteins spanning from the cyan to the infrared part of the spectrum: mCerulean3, mTurquoise2, mT-Sapphire, Clover, mKusabiraOrange2, mOrange2, LSS-mOrange, mRuby2, mBeRFP, mCardinal, iRFP670, NirFP, and iRFP720.
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Affiliation(s)
- Ruth Leben
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), 10117 Berlin, Germany
- Institute of Immunology, Center for Infection Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Randall L. Lindquist
- Immune Dynamics and Intravital Microscopy, Deutsches Rheuma-Forschungszentrum (DRFZ), 10117 Berlin, Germany
- Praxen für Nuklearmedizin, 12163 Berlin, Germany
| | - Anja E. Hauser
- Immune Dynamics and Intravital Microscopy, Deutsches Rheuma-Forschungszentrum (DRFZ), 10117 Berlin, Germany
- Rheumatology and Clinical Immunology, Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), 10117 Berlin, Germany
- Dynamic and Functional In Vivo Imaging, Freie Universität Berlin, 14163 Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), 10117 Berlin, Germany
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10
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Martin E, Suzanne M. mBeRFP: a versatile fluorescent tool to enhance multichannel live imaging and its applications. Development 2022; 149:276390. [DOI: 10.1242/dev.200495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cell and developmental biology increasingly require live imaging of protein dynamics in cells, tissues or living organisms. Thanks to the discovery and development of a panel of fluorescent proteins over the last decades, live imaging has become a powerful and commonly used approach. However, multicolor live imaging remains challenging. The generation of long Stokes shift red fluorescent proteins offers interesting new perspectives to bypass this limitation. Here, we provide a detailed characterization of mBeRFP for in vivo live imaging and its applications in Drosophila. Briefly, we show that a single illumination source is sufficient to stimulate mBeRFP and GFP simultaneously. We demonstrate that mBeRFP can be easily combined with classical green and red fluorescent proteins without any crosstalk. We also show that the low photobleaching of mBeRFP is suitable for live imaging, and that this protein can be used for quantitative applications, such as FRAP or laser ablation. Finally, we believe that this fluorescent protein, with the set of new possibilities it offers, constitutes an important tool for cell, developmental and mechano-biologists in their current research.
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Affiliation(s)
- Emmanuel Martin
- Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS Molecular Cellular and Developmental Biology (MCD) , , 31000 Toulouse , France
| | - Magali Suzanne
- Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS Molecular Cellular and Developmental Biology (MCD) , , 31000 Toulouse , France
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11
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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12
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Kim BB, Wu H, Hao YA, Pan M, Chavarha M, Zhao Y, Westberg M, St-Pierre F, Wu JC, Lin MZ. A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3. Sci Rep 2022; 12:3678. [PMID: 35256624 PMCID: PMC8901740 DOI: 10.1038/s41598-022-07313-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 01/18/2022] [Indexed: 02/07/2023] Open
Abstract
A ratiometric genetically encoded voltage indicator (GEVI) would be desirable for tracking transmembrane voltage changes in the presence of sample motion. We performed combinatorial multi-site mutagenesis on a cyan-excitable red fluorescent protein to create the bright and monomeric mCyRFP3, which proved to be uniquely non-perturbing when fused to the GEVI ASAP3. The green/red ratio from ASAP3-mCyRFP3 (ASAP3-R3) reported voltage while correcting for motion artifacts, allowing the visualization of membrane voltage changes in contracting cardiomyocytes and throughout the cell cycle of motile cells.
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Affiliation(s)
- Benjamin B Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Haodi Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA
- Department of Medicine, Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yukun A Hao
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael Pan
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Mariya Chavarha
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yufeng Zhao
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Michael Westberg
- Department of Neurobiology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Stanford University, Stanford, CA, USA.
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13
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Melzer S, Newmark ER, Mizuno GO, Hyun M, Philson AC, Quiroli E, Righetti B, Gregory MR, Huang KW, Levasseur J, Tian L, Sabatini BL. Bombesin-like peptide recruits disinhibitory cortical circuits and enhances fear memories. Cell 2021; 184:5622-5634.e25. [PMID: 34610277 PMCID: PMC8556345 DOI: 10.1016/j.cell.2021.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 07/12/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023]
Abstract
Disinhibitory neurons throughout the mammalian cortex are powerful enhancers of circuit excitability and plasticity. The differential expression of neuropeptide receptors in disinhibitory, inhibitory, and excitatory neurons suggests that each circuit motif may be controlled by distinct neuropeptidergic systems. Here, we reveal that a bombesin-like neuropeptide, gastrin-releasing peptide (GRP), recruits disinhibitory cortical microcircuits through selective targeting and activation of vasoactive intestinal peptide (VIP)-expressing cells. Using a genetically encoded GRP sensor, optogenetic anterograde stimulation, and trans-synaptic tracing, we reveal that GRP regulates VIP cells most likely via extrasynaptic diffusion from several local and long-range sources. In vivo photometry and CRISPR-Cas9-mediated knockout of the GRP receptor (GRPR) in auditory cortex indicate that VIP cells are strongly recruited by novel sounds and aversive shocks, and GRP-GRPR signaling enhances auditory fear memories. Our data establish peptidergic recruitment of selective disinhibitory cortical microcircuits as a mechanism to regulate fear memories.
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Affiliation(s)
- Sarah Melzer
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Elena R Newmark
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Grace Or Mizuno
- Departments of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Minsuk Hyun
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Adrienne C Philson
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Eleonora Quiroli
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Beatrice Righetti
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Malika R Gregory
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Kee Wui Huang
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - James Levasseur
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Lin Tian
- Departments of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.
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14
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Santos EM, Sheng W, Esmatpour Salmani R, Tahmasebi Nick S, Ghanbarpour A, Gholami H, Vasileiou C, Geiger JH, Borhan B. Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase. J Am Chem Soc 2021; 143:15091-15102. [PMID: 34516091 DOI: 10.1021/jacs.1c05039] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incredible potential for fluorescent proteins to revolutionize biology has inspired the development of a variety of design strategies to address an equally broad range of photophysical characteristics, depending on potential applications. Of these, fluorescent proteins that simultaneously exhibit high quantum yield, red-shifted emission, and wide separation between excitation and emission wavelengths (Large Stokes Shift, LSS) are rare. The pursuit of LSS systems has led to the formation of a complex, obtained from the marriage of a rationally engineered protein (human cellular retinol binding protein II, hCRBPII) and different fluorogenic molecules, capable of supporting photobase activity. The large increase in basicity upon photoexcitation leads to protonation of the fluorophore in the excited state, dramatically red-shifting its emission, leading to an LSS protein/fluorophore complex. Essential for selective photobase activity is the intimate involvement of the target protein structure and sequence that enables Excited State Proton Transfer (ESPT). The potential power and usefulness of the strategy was demonstrated in live cell imaging of human cell lines.
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Affiliation(s)
- Elizabeth M Santos
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - Wei Sheng
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | | | - Setare Tahmasebi Nick
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - Alireza Ghanbarpour
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - Hadi Gholami
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - Chrysoula Vasileiou
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - James H Geiger
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
| | - Babak Borhan
- Michigan State University, Department of Chemistry, East Lansing, Michigan 48824, United States
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15
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Salto R, Giron MD, Puente-Muñoz V, Vilchez JD, Espinar-Barranco L, Valverde-Pozo J, Arosio D, Paredes JM. New Red-Emitting Chloride-Sensitive Fluorescent Protein with Biological Uses. ACS Sens 2021; 6:2563-2573. [PMID: 34148347 PMCID: PMC8478333 DOI: 10.1021/acssensors.1c00094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
A new chloride-sensitive red fluorescent protein derived from Entacmaea quadricolor is described. We found that mBeRFP exhibited moderate sensitivity to chloride and, via site-directed mutagenesis (S94V and R205Y), we increased the chloride affinity by more than an order of magnitude (kd = 106 ± 6 mM) at physiological pH. In addition, cis-trans isomerization of the chromophore produces a dual emission band with different chloride sensitivities, which allowed us to develop a ratiometric methodology to measure intracellular chloride concentrations.
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Affiliation(s)
- Rafael Salto
- Department
of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Unidad
de Excelencia en Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, Cartuja Campus, 18071 Granada, Spain
| | - Maria D. Giron
- Department
of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Unidad
de Excelencia en Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, Cartuja Campus, 18071 Granada, Spain
| | - Virginia Puente-Muñoz
- Department
of Physical Chemistry, Faculty of Pharmacy, Unidad de Excelencia en
Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, C. U. Cartuja, 18071 Granada, Spain
| | - Jose D. Vilchez
- Department
of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Unidad
de Excelencia en Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, Cartuja Campus, 18071 Granada, Spain
| | - Laura Espinar-Barranco
- Department
of Physical Chemistry, Faculty of Pharmacy, Unidad de Excelencia en
Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, C. U. Cartuja, 18071 Granada, Spain
| | - Javier Valverde-Pozo
- Department
of Physical Chemistry, Faculty of Pharmacy, Unidad de Excelencia en
Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, C. U. Cartuja, 18071 Granada, Spain
| | - Daniele Arosio
- Consiglio
Nazionale delle Ricerche (CNR), Istituto di Biofisica (IBF-CNR), 38123 Trento, Italy
| | - Jose M. Paredes
- Department
of Physical Chemistry, Faculty of Pharmacy, Unidad de Excelencia en
Quimica Aplicada a Biomedicina y Medioambiente (UEQ), University of Granada, C. U. Cartuja, 18071 Granada, Spain
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16
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Rigoulot SB, Schimel TM, Lee JH, Sears RG, Brabazon H, Layton JS, Li L, Meier KA, Poindexter MR, Schmid MJ, Seaberry EM, Brabazon JW, Madajian JA, Finander MJ, DiBenedetto J, Occhialini A, Lenaghan SC, Stewart CN. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:830-843. [PMID: 33179383 PMCID: PMC8051605 DOI: 10.1111/pbi.13510] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/31/2020] [Indexed: 05/24/2023]
Abstract
Reverse genetics approaches have revolutionized plant biology and agriculture. Phenomics has the prospect of bridging plant phenotypes with genes, including transgenes, to transform agricultural fields. Genetically encoded fluorescent proteins (FPs) have revolutionized plant biology paradigms in gene expression, protein trafficking and plant physiology. While the first instance of plant canopy imaging of green fluorescent protein (GFP) was performed over 25 years ago, modern phenomics has largely ignored fluorescence as a transgene expression device despite the burgeoning FP colour palette available to plant biologists. Here, we show a new platform for stand-off imaging of plant canopies expressing a wide variety of FP genes. The platform-the fluorescence-inducing laser projector (FILP)-uses an ultra-low-noise camera to image a scene illuminated by compact diode lasers of various colours, coupled with emission filters to resolve individual FPs, to phenotype transgenic plants expressing FP genes. Each of the 20 FPs screened in plants were imaged at >3 m using FILP in a laboratory-based laser range. We also show that pairs of co-expressed fluorescence proteins can be imaged in canopies. The FILP system enabled a rapid synthetic promoter screen: starting from 2000 synthetic promoters transfected into protoplasts to FILP-imaged agroinfiltrated Nicotiana benthamiana plants in a matter of weeks, which was useful to characterize a water stress-inducible synthetic promoter. FILP canopy imaging was also accomplished for stably transformed GFP potato and in a split-GFP assay, which illustrates the flexibility of the instrument for analysing fluorescence signals in plant canopies.
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Affiliation(s)
- Stephen B. Rigoulot
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of MechanicalAerospace and Biomedical EngineeringUniversity of TennesseeKnoxvilleTNUSA
| | - Jun Hyung Lee
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Robert G. Sears
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Holly Brabazon
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Brabazon AppsKnoxvilleTNUSA
| | - Jessica S. Layton
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Li Li
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Kerry A. Meier
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Magen R. Poindexter
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Manuel J. Schmid
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | - Erin M. Seaberry
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
| | | | - Jonathan A. Madajian
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | | | - John DiBenedetto
- Mission Support and Test Services Special Technology LaboratorySanta BarbaraCAUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
- Department of Food ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - C. Neal Stewart
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- Center for Agricultural Synthetic Biology (CASB)University of Tennessee Institute of AgricultureKnoxvilleTNUSA
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17
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Jelcic M, Wang K, Hui KL, Cai XC, Enyedi B, Luo M, Niethammer P. A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. Cell Chem Biol 2020; 27:1073-1083.e12. [PMID: 32521230 DOI: 10.1016/j.chembiol.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/13/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
ATP is an important energy metabolite and allosteric signal in health and disease. ATP-interacting proteins, such as P2 receptors, control inflammation, cell death, migration, and wound healing. However, identification of allosteric ATP sites remains challenging, and our current inventory of ATP-controlled pathways is likely incomplete. Here, we develop and verify mipATP as a minimally invasive photoaffinity probe for ATP-interacting proteins. Its N6 functionalization allows target enrichment by UV crosslinking and conjugation to reporter tags by "click" chemistry. The additions are compact, allowing mipATP to completely retain the calcium signaling responses of native ATP in vitro and in vivo. mipATP specifically enriched for known nucleotide binders in A549 cell lysates and membrane fractions. In addition, it retrieved unannotated ATP interactors, such as the FAS receptor, CD44, and various SLC transporters. Thus, mipATP is a promising tool to identify allosteric ATP sites in the proteome.
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Affiliation(s)
- Mark Jelcic
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ke Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - King Lam Hui
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiao-Chuan Cai
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Balázs Enyedi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Lendület Tissue Damage Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary; HCEMM-SE Inflammatory Signaling Research Group, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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18
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Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ, Trapnell C, Hatch EM, Fowler DM. High-throughput, microscope-based sorting to dissect cellular heterogeneity. Mol Syst Biol 2020; 16:e9442. [PMID: 32500953 PMCID: PMC7273721 DOI: 10.15252/msb.20209442] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence-activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, and then derive their single-cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.
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Affiliation(s)
- Nicholas Hasle
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Sanjay Srivatsan
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Heather Huang
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Jason J Stephany
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Zachary Krieger
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Dana Jackson
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Weiliang Tang
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Sriram Pendyala
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Raymond J Monnat
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of PathologyUniversity of WashingtonSeattleWAUSA
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Emily M Hatch
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Douglas M Fowler
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of BioengineeringUniversity of WashingtonSeattleWAUSA
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19
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Erdogan M, Fabritius A, Basquin J, Griesbeck O. Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells. Cell Chem Biol 2020; 27:610-621.e5. [PMID: 32142629 DOI: 10.1016/j.chembiol.2020.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/22/2019] [Accepted: 02/14/2020] [Indexed: 02/08/2023]
Abstract
Engineered proteins must be phenotypically selected for function in the appropriate physiological context. Here, we present a versatile approach that allows generating panels of mammalian cells that express diversified heterologous protein libraries in the cytosol or subcellular compartments under stable conditions and in a single-variant-per-cell manner. To this end we adapt CRISPR/Cas9 editing technology to diversify targeted stretches of a protein of interest in situ. We demonstrate the utility of the approach by in situ engineering and intra-lysosome specific selection of an extremely pH-resistant long Stokes shift red fluorescent protein variant. Tailoring properties to specific conditions of cellular sub-compartments or organelles of mammalian cells can be an important asset to optimize various proteins, protein-based tools, and biosensors for distinct functions.
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Affiliation(s)
- Mutlu Erdogan
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany.
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20
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Hudson AJ, Wieden HJ. Rapid generation of sequence-diverse terminator libraries and their parameterization using quantitative Term-Seq. Synth Biol (Oxf) 2019; 4:ysz026. [PMID: 32995547 PMCID: PMC7445774 DOI: 10.1093/synbio/ysz026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/03/2019] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology and the rational design and construction of biological devices require vast numbers of characterized biological parts, as well as reliable design tools to build increasingly complex, multigene architectures. Design principles for intrinsic terminators have been established; however, additional sequence-structure studies are needed to refine parameters for termination-based genetic devices. We report a rapid single-pot method to generate libraries of thousands of randomized bidirectional intrinsic terminators and a modified quantitative Term-Seq (qTerm-Seq) method to simultaneously identify terminator sequences and measure their termination efficiencies (TEs). Using qTerm-Seq, we characterize hundreds of additional strong terminators (TE > 90%) with some terminators reducing transcription read-through by up to 1000-fold in Escherichia coli. Our terminator library and qTerm-Seq pipeline constitute a flexible platform enabling identification of terminator parts that can achieve transcription termination not only over a desired range but also to investigate their sequence-structure features, including for specific genetic and application contexts beyond the common in vivo systems such as E. coli.
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Affiliation(s)
- Andrew J Hudson
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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21
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Zhao H, Zhang Y, Pan M, Song Y, Bai L, Miao Y, Huang Y, Zhu X, Song CP. Dynamic imaging of cellular pH and redox homeostasis with a genetically encoded dual-functional biosensor, pHaROS, in yeast. J Biol Chem 2019; 294:15768-15780. [PMID: 31488545 PMCID: PMC6816096 DOI: 10.1074/jbc.ra119.007557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/25/2019] [Indexed: 11/06/2022] Open
Abstract
Intracellular pH and redox states are critical for multiple processes and partly determine cell behavior. Here, we developed a genetically encoded dual-function probe, named p H and redox-sensitive fluorescent protein (pHaROS), for simultaneous real-time detection of changes in redox potential and pH in living cells. pHaROS consists of the Arabidopsis flavin mononucleotide-binding fluorescent protein iLOV and an mKATE variant, mBeRFP. Using pHaROS in Saccharomyces cerevisiae cells, we confirmed that H2O2 raises the overall redox potential of the cell and found that this increase is accompanied by a decrease in cytosolic pH. Furthermore, we observed spatiotemporal pH and redox homeostasis within the nucleus at various stages of the cell cycle in budding yeast (Saccharomyces cerevisiae) during cellular development and responses to oxidative stress. Importantly, we could tailor pHaROS to specific applications, including measurements in different organelles and cell types and the GSH/GSSG ratio, highlighting pHaROS's high flexibility and versatility. In summary, we have developed pHaROS as a dual-function probe that can be used for simultaneously measuring cellular pH and redox potential, representing a very promising tool for determining the cross-talk between intracellular redox- and pH-signaling processes in yeast and mammalian U87 cell.
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Affiliation(s)
- Hang Zhao
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yu Zhang
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Mingming Pan
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yichen Song
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Ling Bai
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yuchen Miao
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yanqin Huang
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Xiaohong Zhu
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Chun-Peng Song
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
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22
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Red-shifted bioluminescence Resonance Energy Transfer: Improved tools and materials for analytical in vivo approaches. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Zhao BQ, Ding WL, Tan ZZ, Tang QY, Zhao KH. A Large Stokes Shift Fluorescent Protein Constructed from the Fusion of Red Fluorescent mCherry and Far-Red Fluorescent BDFP1.6. Chembiochem 2019; 20:1167-1173. [PMID: 30609201 DOI: 10.1002/cbic.201800695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Indexed: 01/17/2023]
Abstract
Phycobiliproteins are constituents of phycobilisomes that can harvest orange, red, and far-red light for photosynthesis in cyanobacteria and red algae. Phycobiliproteins in the phycobilisome cores, such as allophycocyanins, absorb far-red light to funnel energy to the reaction centers. Therefore, allophycocyanin subunits have been engineered as far-red fluorescent proteins, such as BDFP1.6. However, most current fluorescent probes have small Stokes shifts, which limit their applications in multicolor bioimaging. mCherry is an excellent fluorescent protein that has maximal emittance in the red spectral range and a high fluorescence quantum yield, and thus, can be used as a donor for energy transfer to a far-red acceptor, such as BDFP1.6, by FRET. In this study, mCherry was fused with BDFP1.6, which resulted in a highly bright far-red fluorescent protein, BDFP2.0, with a large Stokes shift (≈79 nm). The excitation energy was absorbed maximally at 587 nm by mCherry and transferred to BDFP1.6 efficiently; thus emitting strong far-red fluorescence maximally at 666 nm. The effective brightness of BDFP2.0 in mammalian cells was 4.2-fold higher than that of iRFP670, which has been reported as the brightest far-red fluorescent protein. The large Stokes shift of BDFP2.0 facilitates multicolor bioimaging. Therefore, BDFP2.0 not only biolabels mammalian cells, including human cells, but also biolabels various intracellular components in dual-color imaging.
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Affiliation(s)
- Bao-Qing Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Wen-Long Ding
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zi-Zhu Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qi-Ying Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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24
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Augustine G, Raghavan S, NumbiRamudu K, Easwaramoorthi S, Shanmugam G, Seetharani Murugaiyan J, Gunasekaran K, Govind C, Karunakaran V, Ayyadurai N. Excited State Electronic Interconversion and Structural Transformation of Engineered Red-Emitting Green Fluorescent Protein Mutant. J Phys Chem B 2019; 123:2316-2324. [PMID: 30789731 DOI: 10.1021/acs.jpcb.8b10516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Red fluorescent proteins with a large Stokes shift offer a limited autofluorescence background and are used in deep tissue imaging. Here, by introducing the free amino group in Aequorea victoria, the electrostatic charges of the p-hydroxybenzylidene imidazolinone chromophore of green fluorescent protein (GFP) have been altered resulting in an unusual, 85 nm red-shifted fluorescence. The structural and biophysical analysis suggested that the red shift is due to positional shift occupancy of Glu222 and Arg96, resulting in extended conjugation and a relaxed chromophore. Femtosecond transient absorption spectra exhibited that the excited state relaxation dynamics of red-shifted GFP (rGFP) (τ4 = 234 ps) are faster compared to the A. victoria green fluorescent protein (τ4 = 3.0 ns). The nanosecond time-resolved emission spectra of rGFP reveal the continuous spectral shift during emission by a solvent reorientation in the chromophore. Finally, the molecular dynamics simulations revealed the rearrangement of the hydrogen bond interactions in the chromophore vicinity, reshaping the symmetric distribution of van der Waals space to fine tune the GFP structure resulting from highly red-shifted rGFP.
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Affiliation(s)
- George Augustine
- Department of Biochemistry and Biotechnology , Council of Scientific and Industrial Research-Central Leather Research Institute (CSIR-CLRI) , Chennai 600 020 , India
| | - Sriram Raghavan
- Department of Crystallography and Biophysics , University of Madras , Chennai 600 025 , India
| | - Kamini NumbiRamudu
- Department of Biochemistry and Biotechnology , Council of Scientific and Industrial Research-Central Leather Research Institute (CSIR-CLRI) , Chennai 600 020 , India
| | | | | | | | - Krishnasamy Gunasekaran
- Department of Crystallography and Biophysics , University of Madras , Chennai 600 025 , India
| | - Chinju Govind
- Photosciences and Photonics Section, Chemical Sciences and Technology Division , CSIR-National Institute for Interdisciplinary Science and Technology , Thiruvananthapuram , 695 019 Kerala , India
| | - Venugopal Karunakaran
- Photosciences and Photonics Section, Chemical Sciences and Technology Division , CSIR-National Institute for Interdisciplinary Science and Technology , Thiruvananthapuram , 695 019 Kerala , India
| | - Niraikulam Ayyadurai
- Department of Biochemistry and Biotechnology , Council of Scientific and Industrial Research-Central Leather Research Institute (CSIR-CLRI) , Chennai 600 020 , India
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25
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Zaitseva SO, Farkhutdinova DA, Baleeva NS, Smirnov AY, Zagudaylova MB, Shakhov AM, Astafiev AA, Baranov MS, Bochenkova AV. Excited-state locked amino analogues of the green fluorescent protein chromophore with a giant Stokes shift. RSC Adv 2019; 9:38730-38734. [PMID: 35540244 PMCID: PMC9076007 DOI: 10.1039/c9ra08808c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
We design a new class of excited-state locked GFP chromophores which intrinsically exhibit a very large Stokes shift.
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Affiliation(s)
| | | | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
| | | | | | | | - Artyom A. Astafiev
- Semenov Institute of Chemical Physics of RAS
- Moscow
- Russia
- Department of Chemistry
- Lomonosov Moscow State University
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
- Pirogov Russian National Research Medical University
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26
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Spectral and structural analysis of large Stokes shift fluorescent protein dKeima570. J Microbiol 2018; 56:822-827. [DOI: 10.1007/s12275-018-8319-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 02/05/2023]
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27
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Wang S, Ding M, Xue B, Hou Y, Sun Y. Live Cell Visualization of Multiple Protein-Protein Interactions with BiFC Rainbow. ACS Chem Biol 2018; 13:1180-1188. [PMID: 29283249 DOI: 10.1021/acschembio.7b00931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As one of the most powerful tools to visualize PPIs in living cells, bimolecular fluorescence complementation (BiFC) has gained great advancement during recent years, including deep tissue imaging with far-red or near-infrared fluorescent proteins or super-resolution imaging with photochromic fluorescent proteins. However, little progress has been made toward simultaneous detection and visualization of multiple PPIs in the same cell, mainly due to the spectral crosstalk. In this report, we developed novel BiFC assays based on large-Stokes-shift fluorescent proteins (LSS-FPs) to detect and visualize multiple PPIs in living cells. With the large excitation/emission spectral separation, LSS-FPs can be imaged together with normal Stokes shift fluorescent proteins to realize multicolor BiFC imaging using a simple illumination scheme. We also further demonstrated BiFC rainbow combining newly developed BiFC assays with previously established mCerulean/mVenus-based BiFC assays to achieve detection and visualization of four PPI pairs in the same cell. Additionally, we prove that with the complete spectral separation of mT-Sapphire and CyOFP1, LSS-FP-based BiFC assays can be readily combined with intensity-based FRET measurement to detect ternary protein complex formation with minimal spectral crosstalk. Thus, our newly developed LSS-FP-based BiFC assays not only expand the fluorescent protein toolbox available for BiFC but also facilitate the detection and visualization of multiple protein complex interactions in living cells.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Miao Ding
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingping Hou
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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28
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Kleeman B, Olsson A, Newkold T, Kofron M, DeLay M, Hildeman D, Grimes HL. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry A 2018; 93:556-562. [PMID: 29533508 PMCID: PMC8008483 DOI: 10.1002/cyto.a.23360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/11/2022]
Abstract
The advent of facile genome engineering technologies has made the generation of knock-in gene-expression or fusion-protein reporters more tractable. Fluorescent protein labeling of specific genes combined with surface marker profiling can more specifically identify a cell population. However, the question of which fluorescent proteins to utilize to generate reporter constructs is made difficult by the number of candidate proteins and the lack of updated experimental data on newer fluorescent proteins. Compounding this problem, most fluorescent proteins are designed and tested for use in microscopy. To address this, we cloned and characterized the detection sensitivity, spectral overlap, and spillover spreading of 13 monomeric fluorescent proteins to determine utility in multicolor panels. We identified a group of five fluorescent proteins with high signal to noise ratio, minimal spectral overlap, and low spillover spreading making them compatible for multicolor experiments. Specifically, generating reporters with combinations of three of these proteins would allow efficient measurements even at low-level expression. Because the proteins are monomeric, they could function either as gene-expression or as fusion-protein reporters. Additionally, this approach can be generalized as new fluorescent proteins are developed to determine their usefulness in multicolor panels. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Benjamin Kleeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Tess Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matt Kofron
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - David Hildeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
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29
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Shi H, Luo Q. Biophotonics in China. JOURNAL OF BIOPHOTONICS 2017; 10:1572-1579. [PMID: 29205900 DOI: 10.1002/jbio.201790012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
Biophotonics is a highly interdisciplinary field where physicists, chemists, biologists, physicians and engineers work together to solve the problems appearing in biology and medicine. In China, the Biophotonics discipline is often referred to as Biomedical Photonics, under the first-level disciplines Biomedical Engineering or Optical Engineering, and was initiated in the late 1990s. Over the past 20 years, biophotonics research in China expanded extraordinarily and has reached the frontiers of the world-level sciences. This white paper introduces the research groups in the biophotonics field in China, and their representative contributions.
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Affiliation(s)
- Hua Shi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics (WNLO), Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
- MoE Key Laboratory of Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics (WNLO), Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
- MoE Key Laboratory of Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
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30
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Suzuki K, Nagai T. Recent progress in expanding the chemiluminescent toolbox for bioimaging. Curr Opin Biotechnol 2017; 48:135-141. [DOI: 10.1016/j.copbio.2017.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/31/2022]
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31
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Nuñez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, Federici F. Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. PLoS One 2017; 12:e0187163. [PMID: 29140977 PMCID: PMC5687719 DOI: 10.1371/journal.pone.0187163] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/14/2017] [Indexed: 01/03/2023] Open
Abstract
The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.
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Affiliation(s)
- Isaac Nuñez
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tamara Matute
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Juan Keymer
- Departamento Ecología, Facultad Ciencias Biológicas; Instituto de Física, Facultad de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Timothy Rudge
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail: (TJR); (FF)
| | - Fernán Federici
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
- * E-mail: (TJR); (FF)
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Thorn K. Genetically encoded fluorescent tags. Mol Biol Cell 2017; 28:848-857. [PMID: 28360214 PMCID: PMC5385933 DOI: 10.1091/mbc.e16-07-0504] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 12/25/2022] Open
Abstract
Genetically encoded fluorescent tags are protein sequences that can be fused to a protein of interest to render it fluorescent. These tags have revolutionized cell biology by allowing nearly any protein to be imaged by light microscopy at submicrometer spatial resolution and subsecond time resolution in a live cell or organism. They can also be used to measure protein abundance in thousands to millions of cells using flow cytometry. Here I provide an introduction to the different genetic tags available, including both intrinsically fluorescent proteins and proteins that derive their fluorescence from binding of either endogenous or exogenous fluorophores. I discuss their optical and biological properties and guidelines for choosing appropriate tags for an experiment. Tools for tagging nucleic acid sequences and reporter molecules that detect the presence of different biomolecules are also briefly discussed.
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Affiliation(s)
- Kurt Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
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Shen Y, Chen Y, Wu J, Shaner NC, Campbell RE. Engineering of mCherry variants with long Stokes shift, red-shifted fluorescence, and low cytotoxicity. PLoS One 2017; 12:e0171257. [PMID: 28241009 PMCID: PMC5328254 DOI: 10.1371/journal.pone.0171257] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/17/2017] [Indexed: 01/07/2023] Open
Abstract
MCherry, the Discosoma sp. mushroom coral-derived monomeric red fluorescent protein (RFP), is a commonly used genetically encoded fluorophore for live cell fluorescence imaging. We have used a combination of protein design and directed evolution to develop mCherry variants with low cytotoxicity to Escherichia coli and altered excitation and emission profiles. These efforts ultimately led to a long Stokes shift (LSS)-mCherry variant (λex = 460 nm and λem = 610 nm) and a red-shifted (RDS)-mCherry variant (λex = 600 nm and λem = 630 nm). These new RFPs provide insight into the influence of the chromophore environment on mCherry's fluorescence properties, and may serve as templates for the future development of fluorescent probes for live cell imaging.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yingche Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiahui Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nathan C. Shaner
- Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, United States of America
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Chu J, Oh Y, Sens A, Ataie N, Dana H, Macklin JJ, Laviv T, Welf ES, Dean KM, Zhang F, Kim BB, Tang CT, Hu M, Baird MA, Davidson MW, Kay MA, Fiolka R, Yasuda R, Kim DS, Ng HL, Lin MZ. A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo. Nat Biotechnol 2016; 34:760-7. [PMID: 27240196 PMCID: PMC4942401 DOI: 10.1038/nbt.3550] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/22/2016] [Indexed: 02/02/2023]
Abstract
Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins.
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Affiliation(s)
- Jun Chu
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Younghee Oh
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Pediatrics, Stanford University, Stanford, California, USA
- Department of Neurobiology, Stanford University, Stanford, California, USA
| | - Alex Sens
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Niloufar Ataie
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Hod Dana
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
| | - John J Macklin
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
| | - Tal Laviv
- Max Planck Florida Institute, Jupiter, Florida, USA
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Feijie Zhang
- Department of Pediatrics, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Benjamin B Kim
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Clement Tran Tang
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Michelle Hu
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Michelle A Baird
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Michael W Davidson
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Mark A Kay
- Department of Pediatrics, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Douglas S Kim
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
| | - Ho-Leung Ng
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Pediatrics, Stanford University, Stanford, California, USA
- Department of Neurobiology, Stanford University, Stanford, California, USA
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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36
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Shen Y, Lai T, Campbell RE. Red fluorescent proteins (RFPs) and RFP-based biosensors for neuronal imaging applications. NEUROPHOTONICS 2015; 2:031203. [PMID: 26158012 PMCID: PMC4478792 DOI: 10.1117/1.nph.2.3.031203] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/19/2015] [Indexed: 05/23/2023]
Abstract
The inherent advantages of red-shifted fluorescent proteins and fluorescent protein-based biosensors for the study of signaling processes in neurons and other tissues have motivated the development of a plethora of new tools. Relative to green fluorescent proteins (GFPs) and other blue-shifted alternatives, red fluorescent proteins (RFPs) provide the inherent advantages of lower phototoxicity, lower autofluorescence, and deeper tissue penetration associated with longer wavelength excitation light. All other factors being the same, the multiple benefits of using RFPs make these tools seemingly ideal candidates for use in neurons and, ultimately, the brain. However, for many applications, the practical utility of RFPs still falls short of the preferred GFPs. We present an overview of RFPs and RFP-based biosensors, with an emphasis on their reported applications in neuroscience.
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Affiliation(s)
- Yi Shen
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
| | - Tiffany Lai
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
| | - Robert E. Campbell
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
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D'Angelis do E. S. Barbosa C, Corrêa JR, Medeiros GA, Barreto G, Magalhães KG, de Oliveira AL, Spencer J, Rodrigues MO, Neto BAD. Carbon Dots (C-dots) from Cow Manure with Impressive Subcellular Selectivity Tuned by Simple Chemical Modification. Chemistry 2015; 21:5055-60. [DOI: 10.1002/chem.201406330] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 11/11/2022]
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