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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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Ryan A, Shade O, Bardhan A, Bartnik A, Deiters A. Quantitative Analysis and Optimization of Site-Specific Protein Bioconjugation in Mammalian Cells. Bioconjug Chem 2022; 33:2361-2369. [PMID: 36459098 DOI: 10.1021/acs.bioconjchem.2c00451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Despite a range of covalent protein modifications, few techniques exist for quantification of protein bioconjugation in cells. Here, we describe a novel method for quantifying in cellulo protein bioconjugation through covalent bond formation with HaloTag. This approach utilizes unnatural amino acid (UAA) mutagenesis to selectively install a small and bioorthogonally reactive handle onto the surface of a protein. We utilized the fast kinetics and high selectivity of inverse electron-demand Diels-Alder cycloadditions to evaluate reactions of tetrazine phenylalanine (TetF) with strained trans-cyclooctene-chloroalkane (sTCO-CA) and trans-cyclooctene lysine (TCOK) with tetrazine-chloroalkane (Tet-CA). Following bioconjugation, the chloroalkane ligand is exposed for labeling by the HaloTag enzyme, allowing for straightforward quantification of bioconjugation via simple western blot analysis. We demonstrate the versatility of this tool for quickly and accurately determining the bioconjugation efficiency of different UAA/chloroalkane pairs and for different sites on different proteins of interest, including EGFP and the estrogen-related receptor ERRα.
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Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Aleksander Bartnik
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nat Commun 2022; 13:3825. [PMID: 35780145 PMCID: PMC9250533 DOI: 10.1038/s41467-022-31480-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Human Argonaute 2 (hAgo2) constitutes the functional core of the RNA interference pathway. Guide RNAs direct hAgo2 to target mRNAs, which ultimately leads to hAgo2-mediated mRNA degradation or translational inhibition. Here, we combine site-specifically labeled hAgo2 with time-resolved single-molecule FRET measurements to monitor conformational states and dynamics of hAgo2 and hAgo2-RNA complexes in solution that remained elusive so far. We observe dynamic anchoring and release of the guide’s 3’-end from the PAZ domain during the stepwise target loading process even with a fully complementary target. We find differences in structure and dynamic behavior between partially and fully paired canonical hAgo2-guide/target complexes and the miRNA processing complex formed by hAgo2 and pre-miRNA451. Furthermore, we detect a hitherto unknown conformation of hAgo2-guide/target complexes that poises them for target-directed miRNA degradation. Taken together, our results show how the conformational flexibility of hAgo2-RNA complexes determines function and the fate of the ribonucleoprotein particle. Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
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Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells. Cell Rep 2021; 31:107811. [PMID: 32579937 DOI: 10.1016/j.celrep.2020.107811] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
The pyrrolysyl-tRNA/pyrrolysyl-tRNA synthetase (PylT/RS) pair from the archaeon Methanosarcina mazei (Mma) is widely used in protein engineering to site-specifically introduce noncanonical amino acids (ncAAs) through nonsense codon suppression. Here, we engineer the PylT/RS pair encoded by Methanogenic archaeon ISO4-G1 (G1) to be orthogonal to Mma PylT/RS and alter the G1 PylRS active site to accept a complementary ncAA spectrum. We combine the resulting mutual orthogonal pairs for site-specific dual ncAA incorporation of two lysine analogs with high selectivity and efficiency. Demonstrating the robustness of the system, we incorporate two ncAAs with compatible bioorthogonal reactivity into a Notch receptor, as well as a G protein-coupled receptor. We show that selective and site-specific incorporation of two ncAAs allows for two-color bioorthogonal labeling as well as chemical-controlled crosslinking of surface proteins on live mammalian cells.
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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Biava HD. Tackling Achilles' Heel in Synthetic Biology: Pairing Intracellular Synthesis of Noncanonical Amino Acids with Genetic-Code Expansion to Foster Biotechnological Applications. Chembiochem 2020; 21:1265-1273. [PMID: 31868982 DOI: 10.1002/cbic.201900756] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 12/11/2022]
Abstract
For the last two decades, synthetic biologists have been able to unlock and expand the genetic code, generating proteins with unique properties through the incorporation of noncanonical amino acids (ncAAs). These evolved biomaterials have shown great potential for applications in industrial biocatalysis, therapeutics, bioremediation, bioconjugation, and other areas. Our ability to continue developing such technologies depends on having relatively easy access to ncAAs. However, the synthesis of enantiomerically pure ncAAs in practical quantitates for large-scale processes remains a challenge. Biocatalytic ncAA production has emerged as an excellent alternative to traditional organic synthesis in terms of cost, enantioselectivity, and sustainability. Moreover, biocatalytic synthesis offers the opportunity of coupling the intracellular generation of ncAAs with genetic-code expansion to overcome the limitations of an external supply of amino acid. In this minireview, we examine some of the most relevant achievements of this approach and its implications for improving technological applications derived from synthetic biology.
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Affiliation(s)
- Hernán D Biava
- Department of Science and Mathematics, Brevard College, One Brevard College Drive, Brevard, 28712, NC, USA
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Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells. Biochem Biophys Rep 2018; 17:1-9. [PMID: 30450427 PMCID: PMC6226565 DOI: 10.1016/j.bbrep.2018.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
Many biophysical techniques that are available to study the structure, function and dynamics of cellular constituents require modification of the target molecules. Site-specific labelling of a protein is of particular interest for fluorescence-based single-molecule measurements including single-molecule FRET or super-resolution microscopy. The labelling procedure should be highly specific but minimally invasive to preserve sensitive biomolecules. The modern molecular engineering toolkit provides elegant solutions to achieve the site-specific modification of a protein of interest often necessitating the incorporation of an unnatural amino acid to introduce a unique reactive moiety. The Amber suppression strategy allows the site-specific incorporation of unnatural amino acids into a protein of interest. Recently, this approach has been transferred to the mammalian expression system. Here, we demonstrate how the combination of unnatural amino acid incorporation paired with current bioorthogonal labelling strategies allow the site-specific engineering of fluorescent dyes into proteins produced in the cellular environment of a human cell. We describe in detail which parameters are important to ensure efficient incorporation of unnatural amino acids into a target protein in human expression systems. We furthermore outline purification and bioorthogonal labelling strategies that allow fast protein preparation and labelling of the modified protein. This way, the complete eukaryotic proteome becomes available for single-molecule fluorescence assays. Optimal conditions for incorporation of unnatural amino acids in mammalian cells. Fast small scale purification/labelling for unnatural amino acid-carrying proteins. Evaluation of biorthogonal labelling reactions for dye engineering into proteins.
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Chen B, Su Q, Kong W, Wang Y, Shi P, Wang F. Energy transfer-based biodetection using optical nanomaterials. J Mater Chem B 2018; 6:2924-2944. [DOI: 10.1039/c8tb00614h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review focuses on recent progress in the development of FRET probes and the applications of FRET-based sensing systems.
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Affiliation(s)
- Bing Chen
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Qianqian Su
- Institute of Nanochemistry and Nanobiology
- Shanghai University
- Shanghai 200444
- China
| | - Wei Kong
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Yuan Wang
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
- China
| | - Peng Shi
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
- China
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
| | - Feng Wang
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
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