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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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Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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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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Takahashi T. Generation of Active Protease Depending on Peptide-Protein Interactions Using Interaction-Dependent Native Chemical Ligation and Protein Trans-Splicing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Chemistry and Chemical Biology, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjincho, Kiryu, Gunma 376-8515, Japan
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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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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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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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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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10
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Abstract
Inteins are intervening protein sequences that undergo self-excision from a precursor protein with the concomitant ligation of the flanking polypeptides. Split inteins are expressed in two separated halves, and the recognition and association of two halves are the first crucial step for initiating trans-splicing. In the present study, we carried out the structural and thermodynamic analysis on the interaction of two halves of DnaE split intein from Synechocystis sp. PCC6803. Both isolated halves (IN and IC) are disordered and undergo conformational transition from disorder to order upon association. ITC (isothermal titration calorimetry) reveals that the highly favourable enthalpy change drives the association of the two halves, overcoming the unfavourable entropy change. The high flexibility of two fragments and the marked thermodynamic preference provide a robust association for the formation of the well-folded IN/IC complex, which is the basis for reconstituting the trans-splicing activity of DnaE split intein.
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Aranko AS, Volkmann G. Protein trans-splicing as a protein ligation tool to study protein structure and function. Biomol Concepts 2011; 2:183-98. [DOI: 10.1515/bmc.2011.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 03/10/2011] [Indexed: 01/21/2023] Open
Abstract
AbstractProtein trans-splicing (PTS) exerted by split inteins is a protein ligation reaction which enables overcoming the barriers of conventional heterologous protein production. We provide an overview of the current state-of-the-art in split intein engineering, as well as the achievements of PTS technology in the realm of protein structure-function analyses, including incorporation of natural and artificial protein modifications, controllable protein reconstitution, segmental isotope labeling and protein cyclization. We further discuss factors crucial for the successful implementation of PTS in these protein engineering approaches, and speculate on necessary future endeavours to make PTS a universally applicable protein ligation tool.
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Affiliation(s)
- A. Sesilja Aranko
- 1Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland
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Integrated analysis of receptor activation and downstream signaling with EXTassays. Nat Methods 2009; 7:74-80. [PMID: 20010833 DOI: 10.1038/nmeth.1407] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 11/12/2009] [Indexed: 12/25/2022]
Abstract
The ability to measure multiple cellular signaling events is essential to better understand the underlying complex biological processes that occur in living cells. Microarray-based technologies are now commonly used to study changes in transcription. This information, however, is not sufficient to understand the regulatory mechanisms that lead to gene expression changes. Here we present an approach to monitor signaling events upstream of gene expression. We coupled different reporter gene assays to unique expressed oligonucleotide tags (EXTs) that serve as identifiers and quantitative reporters. Multiple EXT reporters can be isolated as a pool and analyzed by hybridization to microarrays. To test the feasibility of our approach, we integrated complementation assays based on a protease from tobacco etch virus (TEV protease) and transcription factor activity profiling. Thereby, we simultaneously monitored Neuregulin-dependent mouse ErbB receptor tyrosine kinase dimerization, effector recruitment and downstream signaling.
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Müller J, Johnsson N. Split-ubiquitin and the split-protein sensors: chessman for the endgame. Chembiochem 2009; 9:2029-38. [PMID: 18677736 DOI: 10.1002/cbic.200800190] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Judith Müller
- Institute of Medical Biochemistry, Cellular Biochemistry, ZMBE, University of Münster, 48149 Münster, Germany
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Protein interactions: analysis using allele libraries. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:47-66. [PMID: 18528666 DOI: 10.1007/10_2008_102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Interaction defective alleles (IDAs) are alleles that contain mutations affecting their ability to interact with their wild type binding partners. The locations of the mutations may lead to the identification of protein interaction domains and interaction interfaces. IDAs may also distinguish different binding interfaces of multidomain proteins that are part of large complexes, thus shedding light on large protein structures that have yet to be determined. IDAs may also be used in conjunction with RNAi to dissect protein interaction networks. Here, the wild type allele is knocked down and replaced with an IDA that has lost the ability to interact with a specific binding partner. As a result, interactions are disrupted rather than knocking out the entire gene. Thus, IDAs have the potential to be extremely valuable tools in protein interaction network analysis. IDAs can be isolated by reverse two-hybrid analysis, which was demonstrated over a decade ago, but high background levels caused by truncated IDAs have prevented its widespread adoption. We recently described a novel method for full-length allele library generation that eliminates this background and increases the efficiency of the reverse two-hybrid protocol (and IDA isolation) significantly. Here we discuss our strategy for allele library generation, the potential uses of IDAs as outlined above, and additional applications of allele libraries.
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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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Abstract
Lately, scientists have explored approaches to developing fluorescent and/or bioluminescent indicators to pinpoint cellular processes in single living cells. These analytical methods have become a key technology for visualizing and detecting what was otherwise unseen in live cells. The target signaling included second messengers, protein phosphorylations, protein-protein interactions, and protein localizations.
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Affiliation(s)
- Yoshio Umezawa
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.
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Umezawa Y. Methods of Analysis for Imaging and Detecting Ions and Molecules. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Wehr MC, Laage R, Bolz U, Fischer TM, Grünewald S, Scheek S, Bach A, Nave KA, Rossner MJ. Monitoring regulated protein-protein interactions using split TEV. Nat Methods 2006; 3:985-93. [PMID: 17072307 DOI: 10.1038/nmeth967] [Citation(s) in RCA: 208] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 09/20/2006] [Indexed: 11/09/2022]
Abstract
Signaling cascades integrate extracellular stimuli primarily through regulated protein-protein interactions (PPIs). Intracellular signal transduction strictly depends on PPIs occurring at the membrane and in the cytosol. To monitor constitutive and regulated protein interactions within living mammalian cells, we have developed a biological assay termed split TEV. We engineered inactive fragments of the NIa protease from the tobacco etch virus (TEV protease) that regain activity only when coexpressed as fusion constructs with interacting proteins. Functional reconstitution of TEV protease fragments can be monitored with 'proteolysis-only' reporters, which can be previously silent fluorescent and luminescent reporter proteins. Additionally, proteolytically cleavable inactive transcription factors can be combined with any downstream reporter gene of choice to yield 'transcription-coupled' reporter systems. Thus, split TEV combines the advantages of split enzyme- and reporter gene-mediated assays, and provides full flexibility with regard to the final readout. In a first biological application, we monitored neuregulin-induced ErbB2/ErbB4 receptor tyrosine kinase heterodimerization.
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Affiliation(s)
- Michael C Wehr
- Max Planck Institute of Experimental Medicine, Hermann Rein Str. 3, D-37075 Göttingen, Germany
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Lievens S, Lemmens I, Montoye T, Eyckerman S, Tavernier J. Two-hybrid and its recent adaptations. DRUG DISCOVERY TODAY. TECHNOLOGIES 2006; 3:317-324. [PMID: 24980535 DOI: 10.1016/j.ddtec.2006.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interactions between proteins play a pivotal role in virtually all cellular processes, and many of these interactions represent interesting targets for drug development. Among the wide array of interactor-hunting technologies that has emerged, genetic two-hybrid methods account for a large amount of the currently available interaction data and is being successfully applied in interactome-scale mapping projects. Reverse two-hybrid approaches have been developed that allow selected interactions to be assayed for disrupting compounds.:
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Affiliation(s)
- Sam Lievens
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Irma Lemmens
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Tony Montoye
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Sven Eyckerman
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Jan Tavernier
- Flanders Interuniversity Institute for Biotechnology (VIB), Department of Medical Protein Research, Ghent University, Faculty of Medicine and Health Sciences, A. Baertsoenkaai 3, 9000 Ghent, Belgium.
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