1
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Kang C, Shrestha KL, Kwon S, Park S, Kim J, Kwon Y. Intein-Mediated Protein Engineering for Cell-Based Biosensors. BIOSENSORS 2022; 12:bios12050283. [PMID: 35624584 PMCID: PMC9138240 DOI: 10.3390/bios12050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022]
Abstract
Cell-based sensors provide a flexible platform for screening biologically active targets and for monitoring their interactions in live cells. Their applicability extends across a vast array of biological research and clinical applications. Particularly, cell-based sensors are becoming a potent tool in drug discovery and cell-signaling studies by allowing function-based screening of targets in biologically relevant environments and enabling the in vivo visualization of cellular signals in real-time with an outstanding spatiotemporal resolution. In this review, we aim to provide a clear view of current cell-based sensor technologies, their limitations, and how the recent improvements were using intein-mediated protein engineering. We first discuss the characteristics of cell-based sensors and present several representative examples with a focus on their design strategies, which differentiate cell-based sensors from in vitro analytical biosensors. We then describe the application of intein-mediated protein engineering technology for cell-based sensor fabrication. Finally, we explain the characteristics of intein-mediated reactions and present examples of how the intein-mediated reactions are used to improve existing methods and develop new approaches in sensor cell fabrication to address the limitations of current technologies.
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2
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Inteins in Science: Evolution to Application. Microorganisms 2020; 8:microorganisms8122004. [PMID: 33339089 PMCID: PMC7765530 DOI: 10.3390/microorganisms8122004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.
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3
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Abstract
Bioluminescence (BL) is an excellent optical readout platform that has great potential to be utilized in various bioassays and molecular imaging. The advantages of BL-based bioassays include the long dynamic range, minimal background, high signal-to-noise ratios, biocompatibility for use in cell-based assays, no need of external light source for excitation, simplicity in the measurement system, and versatility in the assay design. The recent intensive research in BL has greatly diversified the available luciferase-luciferin systems in the bioassay toolbox. However, the wide variety does not promise their successful utilization in various bioassays as new tools. This is mainly due to complexity and confusion with the diversity, and the unavailability of defined standards. This review is intended to provide an overview of recent basic developments and applications in BL studies, and showcases the bioanalytical utilities. We hope that this review can be used as an instant reference on BL and provides useful guidance for readers in narrowing down their potential options in their own assay designs.
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Affiliation(s)
- Sung-Bae Kim
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine
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4
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Abstract
In recent years, split inteins have seen widespread use as molecular platforms for the design of a variety of peptide and protein chemistry technologies, most notably protein ligation. The development of these approaches is dependent on the identification and/or design of split inteins with robust activity, stability, and solubility. Here, we describe two approaches to characterize and compare the activities of newly identified or engineered split inteins. The first assay employs an E. coli-based selection system to rapidly screen the activities of many inteins and can be repurposed for directed evolution. The second assay utilizes reverse-phase high-performance liquid chromatography (RP-HPLC) to provide insights into individual chemical steps in the protein splicing reaction, information that can guide further engineering efforts. These techniques provide useful alternatives to common assays that utilize SDS-PAGE to analyze splicing reaction progress.
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5
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Sarmiento C, Camarero JA. Biotechnological Applications of Protein Splicing. Curr Protein Pept Sci 2019; 20:408-424. [PMID: 30734675 PMCID: PMC7135711 DOI: 10.2174/1389203720666190208110416] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
Protein splicing domains, also called inteins, have become a powerful biotechnological tool for applications involving molecular biology and protein engineering. Early applications of inteins focused on self-cleaving affinity tags, generation of recombinant polypeptide α-thioesters for the production of semisynthetic proteins and backbone cyclized polypeptides. The discovery of naturallyoccurring split-inteins has allowed the development of novel approaches for the selective modification of proteins both in vitro and in vivo. This review gives a general introduction to protein splicing with a focus on their role in expanding the applications of intein-based technologies in protein engineering and chemical biology.
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Affiliation(s)
- Corina Sarmiento
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA9033 USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA9033 USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-9121, USA
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6
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Di Ventura B, Mootz HD. Switchable inteins for conditional protein splicing. Biol Chem 2018; 400:467-475. [DOI: 10.1515/hsz-2018-0309] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Abstract
Synthetic biologists aim at engineering controllable biological parts such as DNA, RNA and proteins in order to steer biological activities using external inputs. Proteins can be controlled in several ways, for instance by regulating the expression of their encoding genes with small molecules or light. However, post-translationally modifying pre-existing proteins to regulate their function or localization leads to faster responses. Conditional splicing of internal protein domains, termed inteins, is an attractive methodology for this purpose. Here we discuss methods to control intein activity with a focus on those compatible with applications in living cells.
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Affiliation(s)
- Barbara Di Ventura
- Faculty of Biology, University of Freiburg , 79104 Freiburg , Germany
- BIOSS – Centre for Biological Signalling Studies, University of Freiburg , 79104 Freiburg , Germany
| | - Henning D. Mootz
- Department Chemistry and Pharmacy , Institute of Biochemistry, University of Münster , Münster D-48149 , Germany
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7
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Jeon H, Lee E, Kim D, Lee M, Ryu J, Kang C, Kim S, Kwon Y. Cell-Based Biosensors Based on Intein-Mediated Protein Engineering for Detection of Biologically Active Signaling Molecules. Anal Chem 2018; 90:9779-9786. [PMID: 30028129 DOI: 10.1021/acs.analchem.8b01481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Live-cell-based biosensors have emerged as a useful tool for biotechnology and chemical biology. Genetically encoded sensor cells often use bimolecular fluorescence complementation or fluorescence resonance energy transfer to build a reporter unit that suffers from nonspecific signal activation at high concentrations. Here, we designed genetically encoded sensor cells that can report the presence of biologically active molecules via fluorescence-translocation based on split intein-mediated conditional protein trans-splicing (PTS) and conditional protein trans-cleavage (PTC) reactions. In this work, the target molecules or the external stimuli activated intein-mediated reactions, which resulted in activation of the fluorophore-conjugated signal peptide. This approach fully valued the bond-making and bond-breaking features of intein-mediated reactions in sensor construction and thus eliminated the interference of false-positive signals resulting from the mere binding of fragmented reporters. We could also avoid the necessity of designing split reporters to refold into active structures upon reconstitution. These live-cell-based sensors were able to detect biologically active signaling molecules, such as Ca2+ and cortisol, as well as relevant biological stimuli, such as histamine-induced Ca2+ stimuli and the glucocorticoid receptor agonist, dexamethasone. These live-cell-based sensing systems hold large potential for applications such as drug screening and toxicology studies, which require functional information about targets.
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Affiliation(s)
- Hyunjin Jeon
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Euiyeon Lee
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Dahee Kim
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Minhyung Lee
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Jeahee Ryu
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Chungwon Kang
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Soyoun Kim
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
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8
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Yoshimura H, Ozawa T. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Noncoding RNA in Living Cells. Methods Mol Biol 2018; 1649:337-347. [PMID: 29130208 DOI: 10.1007/978-1-4939-7213-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Visualizing RNA in living cells is increasingly important to facilitate accumulation of knowledge about the relation between specific RNA dynamics and physiological events. Single-molecule fluorescence imaging of target RNAs is an excellent approach to analyzing intracellular RNA motion, but it requires special techniques for probe design and microscope setup. Herein, we present a principle and protocol of an RNA visualization probe based on an RNA binding protein of the Pumilio homology domain (PUM-HD). We also describe the setup and operation of a microscope, and introduce an application to visualize telomeric repeats-containing RNA with telomeres and a telomere-related protein: hnRNPA1. This imaging technique is applicable to visualization of different RNAs, especially including repetitive sequences, in living cells.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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9
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10
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Conditional Toxin Splicing Using a Split Intein System. Methods Mol Biol 2016. [PMID: 27714618 DOI: 10.1007/978-1-4939-6451-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein toxin splicing mediated by split inteins can be used as a strategy for conditional cell ablation. The approach requires artificial fragmentation of a potent protein toxin and tethering each toxin fragment to a split intein fragment. The toxin-intein fragments are, in turn, fused to dimerization domains, such that addition of a dimerizing agent reconstitutes the split intein. These chimeric toxin-intein fusions remain nontoxic until the dimerizer is added, resulting in activation of intein splicing and ligation of toxin fragments to form an active toxin. Considerations for the engineering and implementation of conditional toxin splicing (CTS) systems include: choice of toxin split site, split site (extein) chemistry, and temperature sensitivity. The following method outlines design criteria and implementation notes for CTS using a previously engineered system for splicing a toxin called sarcin, as well as for developing alternative CTS systems.
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11
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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12
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Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
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Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
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13
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Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Li Y. Split-inteins and their bioapplications. Biotechnol Lett 2015; 37:2121-37. [DOI: 10.1007/s10529-015-1905-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023]
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15
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Rogers TA, Andrews GE, Jaeger L, Grabow WW. Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer. ACS Synth Biol 2015; 4:162-6. [PMID: 24932527 DOI: 10.1021/sb5000725] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As insights into RNA's many diverse cellular roles continue to be gained, interest and applications in RNA self-assembly and dynamics remain at the forefront of structural biology. The bifurcation of functional molecules into nonfunctional fragments provides a useful strategy for controlling and monitoring cellular RNA processes and functionalities. Herein we present the bifurcation of the preexisting Spinach aptamer and demonstrate its utility as a novel split aptamer system for monitoring RNA self-assembly as well as the processing of pre-short interfering substrates. We show for the first time that the Spinach aptamer can be divided into two nonfunctional halves that, once assembled, restore the original fluorescent signal characteristic of the unabridged aptamer. In this regard, the split-Spinach aptamer is represented as a potential tool for monitoring the self-assembly of artificial and/or natural RNAs.
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Affiliation(s)
- Tucker A. Rogers
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Grant E. Andrews
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
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16
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Yoshimura H, Ozawa T. Methods of Split Reporter Reconstitution for the Analysis of Biomolecules. CHEM REC 2014; 14:492-501. [DOI: 10.1002/tcr.201402001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takeaki Ozawa
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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17
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Topilina NI, Mills KV. Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 2014; 5:5. [PMID: 24490831 PMCID: PMC3922620 DOI: 10.1186/1759-8753-5-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/07/2014] [Indexed: 01/27/2023] Open
Abstract
Intein-mediated protein splicing has become an essential tool in modern biotechnology. Fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. Recent work has extended these in vitro applications to the cell or to whole organisms. We review recent advances in intein-mediated protein expression and modification, post-translational processing and labeling, protein regulation by conditional protein splicing, biosensors, and expression of trans-genes.
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Affiliation(s)
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, 1 College Street, Worcester, MA 01610, USA.
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18
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Alford SC, O'Sullivan C, Obst J, Christie J, Howard PL. Conditional protein splicing of α-sarcin in live cells. MOLECULAR BIOSYSTEMS 2014; 10:831-7. [DOI: 10.1039/c3mb70387h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Ito M, Ozawa T, Takada S. Folding Coupled with Assembly in Split Green Fluorescent Proteins Studied by Structure-based Molecular Simulations. J Phys Chem B 2013; 117:13212-8. [DOI: 10.1021/jp4032817] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mashiho Ito
- Department of Chemistry, School
of Science, The University of Tokyo, Tokyo,
Japan
- Department of Biophysics,
Graduate
School of Science, Kyoto University, Kyoto,
Japan
| | - Takeaki Ozawa
- Department of Chemistry, School
of Science, The University of Tokyo, Tokyo,
Japan
| | - Shoji Takada
- Department of Biophysics,
Graduate
School of Science, Kyoto University, Kyoto,
Japan
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20
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Wong S, Mills E, Truong K. Simultaneous assembly of two target proteins using split inteins for live cell imaging. Protein Eng Des Sel 2013; 26:207-13. [PMID: 23223808 DOI: 10.1093/protein/gzs100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Inteins are protein elements that covalently reassemble proteins from two precursor fragments in a process known as protein splicing. They are commonly used to reassemble a single target protein by protein splicing, but a second target protein can potentially reassemble by intein dimerization. Here, we use the naturally occurring split DnaE intein from Nostoc punctiforme (NpuDnaE) to demonstrate the simultaneous assembly of two target proteins in several examples studied with live cell imaging: yellow fluorescent protein (YFP) with monomeric red fluorescent protein (mRFP), dominant positive mutant of RhoA GTPase with YFP and GCaMP2 Ca(2+) indicator with mRFP. These examples showed the versatility of the strategy along with some interesting attributes: first, the two target proteins are in equal stoichiometry; second, the extent of protein splicing can be reported by a fluorescent protein. In particular, the split GCaMP2 with mRFP could find applications in tissue-specific Ca(2+) imaging in transgenic organisms, where mRFP could control for motion-related intensity changes.
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Affiliation(s)
- Stanley Wong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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21
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Intelligent design of nano-scale molecular imaging agents. Int J Mol Sci 2012; 13:16986-7005. [PMID: 23235326 PMCID: PMC3546735 DOI: 10.3390/ijms131216986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/26/2012] [Indexed: 01/19/2023] Open
Abstract
Visual representation and quantification of biological processes at the cellular and subcellular levels within living subjects are gaining great interest in life science to address frontier issues in pathology and physiology. As intact living subjects do not emit any optical signature, visual representation usually exploits nano-scale imaging agents as the source of image contrast. Many imaging agents have been developed for this purpose, some of which exert nonspecific, passive, and physical interaction with a target. Current research interest in molecular imaging has mainly shifted to fabrication of smartly integrated, specific, and versatile agents that emit fluorescence or luminescence as an optical readout. These agents include luminescent quantum dots (QDs), biofunctional antibodies, and multifunctional nanoparticles. Furthermore, genetically encoded nano-imaging agents embedding fluorescent proteins or luciferases are now gaining popularity. These agents are generated by integrative design of the components, such as luciferase, flexible linker, and receptor to exert a specific on-off switching in the complex context of living subjects. In the present review, we provide an overview of the basic concepts, smart design, and practical contribution of recent nano-scale imaging agents, especially with respect to genetically encoded imaging agents.
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22
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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23
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KAFI AKM, HATTORI MITSURU, OZAWA TAKEAKI. LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS. ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984410000079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the comparison between fluorescent and bioluminescent proteins, advantages and drawbacks of the bioluminescence techniques are described.
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Affiliation(s)
- A. K. M. KAFI
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - MITSURU HATTORI
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - TAKEAKI OZAWA
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, 3-5 Chiyoda-ku, Tokyo 102-0075, Japan
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24
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Sugawara K, Yugami A, Kadoya T, Hosaka K. Electrochemically monitoring the binding of concanavalin A and ovalbumin. Talanta 2011; 85:425-9. [DOI: 10.1016/j.talanta.2011.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/30/2011] [Accepted: 04/01/2011] [Indexed: 11/30/2022]
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Yamada T, Yoshimura H, Inaguma A, Ozawa T. Visualization of Nonengineered Single mRNAs in Living Cells Using Genetically Encoded Fluorescent Probes. Anal Chem 2011; 83:5708-14. [DOI: 10.1021/ac2009405] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Toshimichi Yamada
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asumi Inaguma
- The Department of Structural Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Zhang Y, Yang W, Chen L, Shi Y, Li G, Zhou N. Development of a novel DnaE intein-based assay for quantitative analysis of G-protein-coupled receptor internalization. Anal Biochem 2011; 417:65-72. [PMID: 21726524 DOI: 10.1016/j.ab.2011.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/01/2011] [Accepted: 06/03/2011] [Indexed: 01/12/2023]
Abstract
G-protein-coupled receptor (GPCR) internalization provides a G-protein-subtype-independent method for assaying agonist-stimulated activation of receptors. We have developed a novel assay that allows quantitative analysis of GPCR internalization based on the interaction between activated GPCRs and β-arrestin2 and on Nostoc punctiforme DnaE intein-mediated reconstitution of Renilla luciferase fragments. This assay system was validated using four functionally divergent GPCRs treated with agonists and antagonists. The EC(50) values obtained for the known agonists and antagonists are in close agreement with the results of previous reports, indicating that this assay system is sensitive enough to permit quantification of GPCR internalization. This rapid and quantitative assay, therefore, could be used universally as a functional cell-based assay for GPCR high-throughput screening during drug discovery.
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Affiliation(s)
- Yaping Zhang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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27
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Ozawa T, Umezawa Y. Imaging of endogenous RNA using genetically encoded probes. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2011; 3:27-37. [PMID: 23836587 DOI: 10.1002/9780470559277.ch100152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Imaging of RNAs in single cells revealed their localized transcription and specific function. Such information cannot be obtained from bulk measurements. This unit contains a protocol of an imaging method capable of visualizing endogenous RNAs bound to genetically encoded fluorescent probes in single living cells. The protocol includes methods of design and construction of the probes, their characterization, and imaging a target RNA in living cells. The methods for RNA imaging are generally applicable to many kinds of RNAs and may allow for elucidating novel functions of localized RNAs and understanding their dynamics in living cells. Curr. Protoc. Chem. Biol. 3:27-37 © 2011 by John Wiley & Sons, Inc.
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Affiliation(s)
- Takeaki Ozawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, and Japan Science and Technology Agency, Tokyo, Japan
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28
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Sonntag T, Mootz HD. An intein-cassette integration approach used for the generation of a split TEV protease activated by conditional protein splicing. MOLECULAR BIOSYSTEMS 2011; 7:2031-9. [DOI: 10.1039/c1mb05025g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Abstract
Protein-protein interaction is one of the most pivotal roles of proteins in living organisms. Association/dissociation of proteins reflects responses to intrinsic or extrinsic perturbations of signaling pathways, involved in gene expression, cell division, cell differentiation, and apoptosis. For further understanding of the biological processes, it is important to monitor protein-protein interactions in model organisms. In particular, Escherichia coli-based methods are suitable to assess large libraries of proteins. Many of these proteins cannot be used in yeast due to toxicity or poor expression. Herein we describe a general method based on an intein-mediated protein reconstitution system (PRS) to detect protein-protein interactions in bacterial cells. The PRS-based approach requires no other agents including enzymes, substrates, and ATP. Another advantage is that matured green fluorescent protein (GFP) accumulates in a targeted cell till degraded. These allow highly sensitive screening of protein-protein interactions.
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30
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Functional characterization of a naturally occurring trans-splicing intein from Synechococcus elongatus in a mammalian cell system. Anal Biochem 2010; 407:180-7. [DOI: 10.1016/j.ab.2010.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/11/2010] [Accepted: 08/12/2010] [Indexed: 11/19/2022]
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31
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Ozawa T, Umezawa Y. Peptide Assemblies in Living Cells. Methods for Detecting Protein-Protein Interactions†. Supramol Chem 2010. [DOI: 10.1080/10610270290026185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Takeaki Ozawa
- a Department of Chemistry, School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
- b Japan Science and Technology Corporation , Tokyo , Japan
| | - Yoshio Umezawa
- a Department of Chemistry, School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
- b Japan Science and Technology Corporation , Tokyo , Japan
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32
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33
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Kim SB, Ozawa T. Creating bioluminescent indicators to visualise biological events in living cells and animals. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.485251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Misawa N, Kafi AKM, Hattori M, Miura K, Masuda K, Ozawa T. Rapid and High-Sensitivity Cell-Based Assays of Protein−Protein Interactions Using Split Click Beetle Luciferase Complementation: An Approach to the Study of G-Protein-Coupled Receptors. Anal Chem 2010; 82:2552-60. [DOI: 10.1021/ac100104q] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naomi Misawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - A. K. M. Kafi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Mitsuru Hattori
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Kenji Miura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Kenji Masuda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, ProbeX Inc., 4-1-4 Bunkyo-ku, Hongo, Tokyo 113-0033, Japan, PRESTO, Japan Science and Technology Agency, 5-3 Chiyoda-ku Yonbanchou, Tokyo 102-8666, Japan, and Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24, Toyo-cho, Tsuruga, Fukui, 914-0047, Japan
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35
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Affiliation(s)
- Henning D Mootz
- Technische Universität Dortmund, Fakultät Chemie, Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.
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36
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Wang H, Nakata E, Hamachi I. Recent progress in strategies for the creation of protein-based fluorescent biosensors. Chembiochem 2010; 10:2560-77. [PMID: 19693761 DOI: 10.1002/cbic.200900249] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The creation of novel bioanalytical tools for the detection and monitoring of a range of important target substances and biological events in vivo and in vitro is a great challenge in chemical biology and biotechnology. Protein-based fluorescent biosensors--integrated devices that convert a molecular-recognition event to a fluorescent signal--have recently emerged as a powerful tool. As the recognition units various proteins that can specifically recognize and bind a variety of molecules of biological significance with high affinity are employed. For the transducer, fluorescent proteins, such as green fluorescent protein (GFP) or synthetic fluorophores, are mostly adopted. Recent progress in protein engineering and organic synthesis allows us to manipulate proteins genetically and/or chemically, and a library of such protein scaffolds has been significantly expanded by genome projects. In this review, we briefly describe the recent progress of protein-based fluorescent biosensors on the basis of their platform and construction strategy, which are primarily divided into the genetically encoded fluorescent biosensors and chemically constructed biosensors.
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Affiliation(s)
- Hangxiang Wang
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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37
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Kerppola TK. Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation. Chem Soc Rev 2009; 38:2876-86. [PMID: 19771334 PMCID: PMC2980501 DOI: 10.1039/b909638h] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigations of the molecular processes that sustain life must include studies of these processes in their normal cellular environment. The bimolecular fluorescence complementation (BiFC) assay provides an approach for the visualization of protein interactions and modifications in living cells. This assay is based on the facilitated association of complementary fragments of a fluorescent protein that are fused to interaction partners. Complex formation by the interaction partners tethers the fluorescent protein fragments in proximity to each other, which can facilitate their association. The BiFC assay enables sensitive visualization of protein complexes with high spatial resolution. The temporal resolution of BiFC analysis is limited by the time required for fluorophore formation, as well as the stabilization of complexes by association of the fluorescent protein fragments. Many modifications and enhancements to the BiFC assay have been developed. The multicolor BiFC assay enables simultaneous visualization of multiple protein complexes in the same cell, and can be used to investigate competition among mutually exclusive interaction partners for complex formation in cells. The ubiquitin-mediated fluorescence complementation (UbFC) assay enables visualization of covalent ubiquitin family peptide conjugation to substrate proteins in cells. The BiFC assay can also be used to visualize protein binding to specific chromatin domains, as well as other molecular scaffolds in cells. BiFC analysis therefore provides a powerful approach for the visualization of a variety of processes that affect molecular proximity in living cells. The visualization of macromolecular interactions and modifications is of great importance owing to the central roles of proteins, nucleic acids and other macromolecular complexes in the regulation of cellular functions. This tutorial review describes the BiFC assay, and discusses the advantages and disadvantages of this experimental approach. The review will be of interest to scientists interested in the investigation of macromolecular interactions or modifications who need exquisite sensitivity for the detection of their complexes or conjugates of interest.
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Affiliation(s)
- Tom K Kerppola
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0650, USA.
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38
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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39
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Fluorescence complementation via EF-hand interactions. J Biotechnol 2009; 142:205-13. [PMID: 19500621 DOI: 10.1016/j.jbiotec.2009.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 05/06/2009] [Accepted: 05/12/2009] [Indexed: 11/20/2022]
Abstract
Fluorescence complementation technology with fluorescent proteins is a powerful approach to investigate molecular recognition by monitoring fluorescence enhancement when non-fluorescent fragments of fluorescent proteins are fused with target proteins, resulting in a new fluorescent complex. Extension of the technology to calcium-dependent protein-protein interactions has, however, rarely been reported. Here, a linker containing trypsin cleavage sites was grafted onto enhanced green fluorescent protein (EGFP). Under physiological conditions, a modified fluorescent protein, EGFP-T1, was cleaved into two major fragments which continue to interact with each other, exhibiting strong optical and fluorescence signals. The larger fragment, comprised of amino acids 1-172, including the chromophore, retains only weak fluorescence. Strong green fluorescence was observed when plasmid DNA encoding complementary EGFP fragments fused to the EF-hand motifs of calbindin D9k (EF1 and EF2) were co-transfected into HeLa cells, suggesting that chromophore maturation and fluorescence complementation from EGFP fragments can be accomplished intracellularly by reassembly of EF-hand motifs, which have a strong tendency for dimerization. Moreover, an intracellular calcium increase upon addition of a calcium ionophore, ionomycin in living cells, results in an increase of fluorescence signal. This novel application of calcium-dependent fluorescence complementation has the potential to monitor protein-protein interactions triggered by calcium signalling pathways in living cells.
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40
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Huang YM, Bystroff C. Complementation and reconstitution of fluorescence from circularly permuted and truncated green fluorescent protein. Biochemistry 2009; 48:929-40. [PMID: 19140681 DOI: 10.1021/bi802027g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Green fluorescent protein (GFP) has been used as a proof of concept for a novel "leave-one-out" biosensor design in which a protein that has a segment omitted from the middle of the sequence by circular permutation and truncation binds the missing peptide and reconstitutes its function. Three variants of GFP have been synthesized that are each missing one of the 11 beta-strands from its beta-barrel structure, and in two of the variants, adding the omitted peptide sequence in trans reconstitutes fluorescence. Detailed biochemical analysis indicates that GFP with beta-strand 7 "left out" (t7SPm) exists in a partially unfolded state. The apo form t7SPm binds the free beta-strand 7 peptide with a dissociation constant of approximately 0.5 microM and folds into the native state of GFP, resulting in fluorescence recovery. Folding of t7SPm, both with and without the peptide ligand, is at least a three-state process and has a rate comparable to that of the full-length and unpermuted GFP. The conserved kinetic properties strongly suggest that the rate-limiting steps in the folding pathway have not been altered by circular permutation and truncation in t7SPm. This study shows that structural and functional reconstitution of GFP can occur with a segment omitted from the middle of the chain, and that the unbound form is in a partially unfolded state.
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Affiliation(s)
- Yao-ming Huang
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, USA
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41
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OZAWA T. Protein Reconstitution Methods for Visualizing Biomolecular Function in Living Cells. YAKUGAKU ZASSHI 2009; 129:289-95. [DOI: 10.1248/yakushi.129.289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takeaki OZAWA
- Department of Chemistry, School of Science, The University of Tokyo
- PRESTO, Japan Science and Technology Agency
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42
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2305] [Impact Index Per Article: 153.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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43
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Mechanische Kontrolle des Entfaltungspfades des grün fluoreszierenden Proteins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Bertz M, Kunfermann A, Rief M. Navigating the Folding Energy Landscape of Green Fluorescent Protein. Angew Chem Int Ed Engl 2008; 47:8192-5. [DOI: 10.1002/anie.200802987] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Loving G, Imperiali B. A versatile amino acid analogue of the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide: a powerful tool for the study of dynamic protein interactions. J Am Chem Soc 2008; 130:13630-8. [PMID: 18808123 DOI: 10.1021/ja804754y] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new unnatural amino acid based on the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) for application in the study of protein-protein interactions. The fluorescence quantum yield of this chromophore is highly sensitive to changes in the local solvent environment, demonstrating "switch-like" emission properties characteristic of the dimethylaminophthalimide family of fluorophores. In particular, this new species possesses a number of significant advantages over related fluorophores, including greater chemical stability under a wide range of conditions, a longer wavelength of excitation (408 nm), and improved synthetic accessibility. This amino acid has been prepared as an Fmoc-protected building block and may readily be incorporated into peptides via standard solid-phase peptide synthesis. A series of comparative studies are presented to demonstrate the advantageous properties of the 4-DMN amino acid relative to those of the previously reported 4-N,N-dimethylaminophthalimidoalanine and 6-N,N-dimethylamino-2,3-naphthalimidoalanine amino acids. Other commercially available solvatochromic fluorophores are also include in these studies. The potential of this new probe as a tool for the study of protein-protein interactions is demonstrated by introducing it into a peptide that is recognized by calcium-activated calmodulin. The binding interaction between these two components yields an increase in fluorescence emission greater than 900-fold.
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Affiliation(s)
- Galen Loving
- Department of Chemistry, Massachusetts Institute of Technology, 77 Mass Avenue, Cambridge, Massachusetts 02139, USA
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46
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Coppola JM, Ross BD, Rehemtulla A. Noninvasive imaging of apoptosis and its application in cancer therapeutics. Clin Cancer Res 2008; 14:2492-501. [PMID: 18413842 DOI: 10.1158/1078-0432.ccr-07-0782] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Activation of the apoptotic cascade plays an important role in the response of tumors to therapy. Noninvasive imaging of apoptosis facilitates optimization of therapeutic protocols regarding dosing and schedule and enables identification of efficacious combination therapies. EXPERIMENTAL DESIGN We describe a hybrid polypeptide that reports on caspase-3 activity in living cells and animals in a noninvasive manner. This reporter, ANLucBCLuc, constitutes a fusion of small interacting peptides, peptide A and peptide B, with the NLuc and CLuc fragments of luciferase with a caspase-3 cleavage site (DEVD) between pepANLuc (ANLuc) and pepBCLuc (BCLuc). During apoptosis, caspase-3 cleaves the reporter, enabling separation of ANLuc from BCLuc. A high-affinity interaction between peptide A and peptide B restores luciferase activity by NLuc and CLuc complementation. Using a D54 glioma model, we show the utility of the reporter in imaging of apoptosis in living subjects in response to various chemotherapy and radiotherapy regimens. RESULTS Treatment of live cells and mice carrying D54 tumor xenografts with chemotherapeutic agents such as temozolomide and perifosine resulted in induction of bioluminescence activity, which correlated with activation of caspase-3. Treatment of mice with combination therapy of temozolomide and radiation resulted in increased bioluminescence activity over individual treatments and increased therapeutic response due to enhanced apoptosis. CONCLUSION The data provided show the utility of the ANLucBCLuc reporter in dynamic, noninvasive imaging of apoptosis and provides a rationale for use of this technology to optimize dose and schedule of novel therapies or to develop novel combination therapies using existing drugs.
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Affiliation(s)
- Julia M Coppola
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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47
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Valencia-Burton M, Broude NE. Visualization of RNA using fluorescence complementation triggered by aptamer-protein interactions (RFAP) in live bacterial cells. ACTA ACUST UNITED AC 2008; Chapter 17:Unit 17.11. [PMID: 18228500 DOI: 10.1002/0471143030.cb1711s37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit describes a method allowing RNA visualization in live cells. The method is based on fluorescent protein complementation regulated by RNA-aptamer/RNA-binding protein interactions. Based on these two principles, a fluorescent ribonucleoprotein complex is assembled inside the cell only in response to the presence of the aptamer sequence on the target RNA.
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Affiliation(s)
- Maria Valencia-Burton
- Center for Advanced Biotechnology, College of Engineering, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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48
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Villalobos V, Naik S, Piwnica-Worms D. Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation. Methods Mol Biol 2008; 439:339-352. [PMID: 18370114 DOI: 10.1007/978-1-59745-188-8_23] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Protein fragment complementation has emerged as a powerful tool for measuring protein-protein interactions in the context of live cells. The adaptation of this strategy for use with firefly luciferase now allows for the non-invasive, quantitative, real-time readout of protein interactions in lysates, live cells, and whole animals. Bioluminescence provides a robust imaging modality due to its extremely low background signal and large dynamic range. The split luciferase fusion constructs described here are inducible by addition of ligands, small molecules or drugs, in this example, rapamycin, and have been shown to work in vivo.
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Affiliation(s)
- Victor Villalobos
- Molecular Imaging Center, Mallinckrodt Institute of Radiology, St. Louis, MO, USA
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49
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Umezawa Y. Optical probes for molecular processes in live cells. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:397-421. [PMID: 20636084 DOI: 10.1146/annurev.anchem.1.031207.112757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this review, I summarize the development over the past several years of fluorescent and/or bioluminescent indicators to pinpoint cellular processes in living cells. These processes involve second messengers, protein phosphorylations, protein-protein interactions, protein-ligand interactions, nuclear receptor-coregulator interactions, nucleocytoplasmic trafficking of functional proteins, and protein localization.
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50
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Ando T, Tsukiji S, Tanaka T, Nagamune T. Construction of a small-molecule-integrated semisynthetic split intein for in vivo protein ligation. Chem Commun (Camb) 2007:4995-7. [PMID: 18049731 DOI: 10.1039/b712843f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new split intein-based protein ligation tool that is synthetically accessible and can be used for protein semisynthesis on the cell surface and potentially inside cells has been constructed.
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Affiliation(s)
- Tomomi Ando
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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