1
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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Gulyak EL, Alferova VA, Korshun VA, Sapozhnikova KA. Introduction of Carbonyl Groups into Antibodies. Molecules 2023; 28:7890. [PMID: 38067618 PMCID: PMC10707781 DOI: 10.3390/molecules28237890] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Antibodies and their derivatives (scFv, Fabs, etc.) represent a unique class of biomolecules that combine selectivity with the ability to target drug delivery. Currently, one of the most promising endeavors in this field is the development of molecular diagnostic tools and antibody-based therapeutic agents, including antibody-drug conjugates (ADCs). To meet this challenge, it is imperative to advance methods for modifying antibodies. A particularly promising strategy involves the introduction of carbonyl groups into the antibody that are amenable to further modification by biorthogonal reactions, namely aliphatic, aromatic, and α-oxo aldehydes, as well as aliphatic and aryl-alkyl ketones. In this review, we summarize the preparation methods and applications of site-specific antibody conjugates that are synthesized using this approach.
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Affiliation(s)
| | | | | | - Ksenia A. Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.L.G.); (V.A.A.); (V.A.K.)
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4
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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5
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Fatema N, Fan C. Studying lysine acetylation of citric acid cycle enzymes by genetic code expansion. Mol Microbiol 2023; 119:551-559. [PMID: 36890576 PMCID: PMC10636775 DOI: 10.1111/mmi.15052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Lysine acetylation is one of the most abundant post-translational modifications in nature, affecting many key biological pathways in both prokaryotes and eukaryotes. It has not been long since technological advances led to understanding of the roles of acetylation in biological processes. Most of those studies were based on proteomic analyses, which have identified thousands of acetylation sites in a wide range of proteins. However, the specific role of individual acetylation event remains largely unclear, mostly due to the existence of multiple acetylation and dynamic changes of acetylation levels. To solve these problems, the genetic code expansion technique has been applied in protein acetylation studies, facilitating the incorporation of acetyllysine into a specific lysine position to generate a site-specifically acetylated protein. By this method, the effects of acetylation at a specific lysine residue can be characterized with minimal interferences. Here, we summarized the development of the genetic code expansion technique for lysine acetylation and recent studies on lysine acetylation of citrate acid cycle enzymes in bacteria by this approach, providing a practical application of the genetic code expansion technique in protein acetylation studies.
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Affiliation(s)
- Nour Fatema
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
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6
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Hiefinger C, Mandl S, Wieland M, Kneuttinger A. Rational design, production and in vitro analysis of photoxenoproteins. Methods Enzymol 2023; 682:247-288. [PMID: 36948704 DOI: 10.1016/bs.mie.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In synthetic biology, the artificial control of proteins by light is of growing interest since it enables the spatio-temporal regulation of downstream molecular processes. This precise photocontrol can be established by the site-directed incorporation of photo-sensitive non-canonical amino acids (ncAAs) into proteins, which generates so-called photoxenoproteins. Photoxenoproteins can be engineered using ncAAs that facilitate the irreversible activation or reversible regulation of their activity upon irradiation. In this chapter, we provide a general outline of the engineering process based on the current methodological state-of-the-art to obtain artificial photocontrol in proteins using the ncAAs o-nitrobenzyl-O-tyrosine as example for photocaged ncAAs (irreversible), and phenylalanine-4'-azobenzene as example for photoswitchable ncAAs (reversible). We thereby focus on the initial design as well as the production and characterization of photoxenoproteins in vitro. Finally, we outline the analysis of photocontrol under steady-state and non-steady-state conditions using the allosteric enzyme complexes imidazole glycerol phosphate synthase and tryptophan synthase as examples.
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Affiliation(s)
- Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sabrina Mandl
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Wieland
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Kneuttinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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7
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Marx A, Julier A, Radtke V, Scheffner M. Generation and characterization of site-specifically mono-ubiquitylated p53. Chembiochem 2022; 23:e202100659. [PMID: 35025136 PMCID: PMC9303418 DOI: 10.1002/cbic.202100659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/12/2022] [Indexed: 11/11/2022]
Abstract
The tumor suppressor p53 is regulated by various posttranslational modifications including different types of ubiquitylation, which exert distinct effects on p53. While modification by ubiquitin chains targets p53 for degradation, attachment of single ubiquitin moieties (mono‐ubiquitylation) affects the intracellular location of p53 and/or its interaction with chromatin. However, how this is achieved at the molecular level remains largely unknown. Similarly, since p53 can be ubiquitylated at different lysine residues, it remains unclear if the eventual effect depends on the position of the lysine modified. Here, we combined genetic code expansion with oxime ligation to generate p53 site‐specifically mono‐ubiquitylated at position 120. We found that mono‐ubiquitylation at this position neither interferes with p53 ubiquitylation by the E3 ligases HDM2 and E6AP in complex with the viral E6 oncoprotein nor affects p53 binding to a cognate DNA sequence. Thus, ubiquitylation per se does not affect physiologically relevant properties of p53.
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Affiliation(s)
- Andreas Marx
- Konstanz University, Department of Chemistry, Universitaetsstrasse 10, 78457, Konstanz, GERMANY
| | | | - Vanessa Radtke
- University of Konstanz: Universitat Konstanz, Chemistry, GERMANY
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8
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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9
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Neumann-Staubitz P, Lammers M, Neumann H. Genetic Code Expansion Tools to Study Lysine Acylation. Adv Biol (Weinh) 2021; 5:e2100926. [PMID: 34713630 DOI: 10.1002/adbi.202100926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022]
Abstract
Lysine acylation is a ubiquitous protein modification that controls various aspects of protein function, such as the activity, localization, and stability of enzymes. Mass spectrometric identification of lysine acylations has witnessed tremendous improvements in sensitivity over the last decade, facilitating the discovery of thousands of lysine acylation sites in proteins involved in all essential cellular functions across organisms of all domains of life. However, the vast majority of currently known acylation sites are of unknown function. Semi-synthetic methods for installing lysine derivatives are ideally suited for in vitro experiments, while genetic code expansion (GCE) allows the installation and study of such lysine modifications, especially their dynamic properties, in vivo. An overview of the current state of the art is provided, and its potential is illustrated with case studies from recent literature. These include the application of engineered enzymes and GCE to install lysine modifications or photoactivatable crosslinker amino acids. Their use in the context of central metabolism, bacterial and viral pathogenicity, the cytoskeleton and chromatin dynamics, is investigated.
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Affiliation(s)
- Petra Neumann-Staubitz
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
| | - Michael Lammers
- Institute for Biochemistry, Department Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Heinz Neumann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
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10
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Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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11
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Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
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Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
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12
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Tharp JM, Hampton JT, Reed CA, Ehnbom A, Chen PHC, Morse JS, Kurra Y, Pérez LM, Xu S, Liu WR. An amber obligate active site-directed ligand evolution technique for phage display. Nat Commun 2020; 11:1392. [PMID: 32170178 PMCID: PMC7070036 DOI: 10.1038/s41467-020-15057-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/14/2020] [Indexed: 01/19/2023] Open
Abstract
Although noncanonical amino acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two decades ago, their application for use in drug discovery has been limited due to inherent library bias towards sense-containing phages. Here, we report a technique based on superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias that has hindered incorporation of ncAAs into phage libraries. We then take advantage of this technique for development of active site-directed ligand evolution of peptides, where the ncAA serves as an anchor to direct the binding of its peptides to the target’s active site. To demonstrate this, phage-displayed peptide libraries are developed that contain a genetically encoded butyryl lysine and are subsequently used to select for ligands that bind SIRT2. These ligands are then modified to develop low nanomolar inhibitors of SIRT2. Most epigenetic regulator inhibitors target tunnels of active sites, rather than the peptide binding groove, leading to concerns with low selectivity. Here the authors use an amber obligate phage library to rapidly identify isoform-selective inhibitors of SIRT2.
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Affiliation(s)
- Jeffery M Tharp
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - J Trae Hampton
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Catrina A Reed
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Andreas Ehnbom
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Peng-Hsun Chase Chen
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jared S Morse
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yadagirri Kurra
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lisa M Pérez
- Laboratory for Molecular Simulation, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA. .,Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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13
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Chen H, Venkat S, McGuire P, Gan Q, Fan C. Recent Development of Genetic Code Expansion for Posttranslational Modification Studies. Molecules 2018; 23:E1662. [PMID: 29986538 PMCID: PMC6100177 DOI: 10.3390/molecules23071662] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022] Open
Abstract
Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Sumana Venkat
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Paige McGuire
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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14
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Abstract
As an important epigenetic mark, lysine methylations play critical roles in the regulation of both chromatin and non-chromatin proteins. There are three levels of lysine methylation, mono-, di-, and trimethylation. Each one has turned out to be biologically distinctive. For the biochemical characterization of proteins with lysine methylation, multiple chemical biology methods have been developed. This concept article will highlight these developments and their applications in epigenetic investigation of protein functions.
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Affiliation(s)
- Zhipeng A. Wang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R. Liu
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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15
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Abstract
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.
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Affiliation(s)
- Dominik K Kölmel
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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16
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Wong HE, Pack SP, Kwon I. Positional effects of hydrophobic non-natural amino acid mutagenesis into the surface region of murine dihydrofolate reductase on enzyme properties. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Spears RJ, Fascione MA. Site-selective incorporation and ligation of protein aldehydes. Org Biomol Chem 2016; 14:7622-38. [DOI: 10.1039/c6ob00778c] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The incorporation of aldehyde handles into proteins, and subsequent chemical reactions thereof, is rapidly proving to be an effective way of generating homogeneous, covalently linked protein constructs that can display a vast array of functionality.
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18
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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19
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Lim SI, Kwon I. Bioconjugation of therapeutic proteins and enzymes using the expanded set of genetically encoded amino acids. Crit Rev Biotechnol 2015; 36:803-15. [DOI: 10.3109/07388551.2015.1048504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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20
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Tuley A, Lee YJ, Wu B, Wang ZU, Liu WR. A genetically encoded aldehyde for rapid protein labelling. Chem Commun (Camb) 2015; 50:7424-6. [PMID: 24756176 DOI: 10.1039/c4cc02000f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair, 3-formyl-phenylalanine is genetically incorporated into proteins at amber mutation sites in Escherichia coli. This non-canonical amino acid readily reacts with hydroxylamine dyes, leading to rapid and site-selective protein labelling.
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Affiliation(s)
- Alfred Tuley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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21
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Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment - Expanding the chemistry in biology. Chem Sci 2015; 6:50-69. [PMID: 28553457 PMCID: PMC5424465 DOI: 10.1039/c4sc01534g] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022] Open
Abstract
Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of 'non-sense' codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.
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Affiliation(s)
- Anaëlle Dumas
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Lukas Lercher
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher D Spicer
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Benjamin G Davis
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
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22
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Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun 2014; 5:4740. [PMID: 25190082 DOI: 10.1038/ncomms5740] [Citation(s) in RCA: 718] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.
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Affiliation(s)
- Christopher D Spicer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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23
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Torres-Kolbus J, Chou C, Liu J, Deiters A. Synthesis of non-linear protein dimers through a genetically encoded Thiol-ene reaction. PLoS One 2014; 9:e105467. [PMID: 25181502 PMCID: PMC4152134 DOI: 10.1371/journal.pone.0105467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/21/2014] [Indexed: 11/19/2022] Open
Abstract
Site-specific incorporation of bioorthogonal unnatural amino acids into proteins provides a useful tool for the installation of specific functionalities that will allow for the labeling of proteins with virtually any probe. We demonstrate the genetic encoding of a set of alkene lysines using the orthogonal PylRS/PylTCUA pair in Escherichia coli. The installed double bond functionality was then applied in a photoinitiated thiol-ene reaction of the protein with a fluorescent thiol-bearing probe, as well as a cysteine residue of a second protein, showing the applicability of this approach in the formation of heterogeneous non-linear fused proteins.
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Affiliation(s)
- Jessica Torres-Kolbus
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chungjung Chou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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24
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Zeng Y, Wang W, Liu WR. Towards reassigning the rare AGG codon in Escherichia coli. Chembiochem 2014; 15:1750-4. [PMID: 25044341 DOI: 10.1002/cbic.201400075] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Indexed: 11/09/2022]
Abstract
The rare AGG codon in Escherichia coli has been reassigned to code non-canonical amino acids (ncAAs) by using the PylRS-tRNA(Pyl)(CCU) pair. When N(ε) -alloc-lysine was used as a PylRS substrate, almost quantitative occupancy of N(ε) -alloc-lysine at an AGG codon site was achieved in minimal medium. ncAAs can be potentially incorporated at the AGG codon with varying efficiencies, depending on their activities towards corresponding enzymes. As AGG is a sense codon, the approach reported here resolves the typical low ncAA incorporation issue that has been associated with ncAA mutagenesis and therefore allows bulk preparation of proteins with site-selectively incorporated ncAAs for applications such as therapeutic protein production.
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Affiliation(s)
- Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX 77843 (USA)
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25
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Furman J, Kang M, Choi S, Cao Y, Wold ED, Sun SB, Smider V, Schultz PG, Kim CH. A genetically encoded aza-Michael acceptor for covalent cross-linking of protein-receptor complexes. J Am Chem Soc 2014; 136:8411-7. [PMID: 24846839 PMCID: PMC4227728 DOI: 10.1021/ja502851h] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 12/31/2022]
Abstract
Selective covalent bond formation at a protein-protein interface potentially can be achieved by genetically introducing into a protein an appropriately "tuned" electrophilic unnatural amino acid that reacts with a native nucleophilic residue in its cognate receptor upon complex formation. We have evolved orthogonal aminoacyl-tRNA synthetase/tRNACUA pairs that genetically encode three aza-Michael acceptor amino acids, N(ε)-acryloyl-(S)-lysine (AcrK, 1), p-acrylamido-(S)-phenylalanine (AcrF, 2), and p-vinylsulfonamido-(S)-phenylalanine (VSF, 3), in response to the amber stop codon in Escherichia coli. Using an αErbB2 Fab-ErbB2 antibody-receptor pair as an example, we demonstrate covalent bond formation between an αErbB2-VSF mutant and a specific surface lysine ε-amino group of ErbB2, leading to near quantitative cross-linking to either purified ErbB2 in vitro or to native cellular ErbB2 at physiological pH. This efficient biocompatible reaction may be useful for creating novel cell biological probes, diagnostics, or therapeutics that selectively and irreversibly bind a target protein in vitro or in living cells.
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Affiliation(s)
- Jennifer
L. Furman
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mingchao Kang
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Seihyun Choi
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Cao
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Erik D. Wold
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sophie B. Sun
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Vaughn
V. Smider
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G. Schultz
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Chan Hyuk Kim
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
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26
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 797] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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27
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Wan W, Tharp JM, Liu WR. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1059-70. [PMID: 24631543 DOI: 10.1016/j.bbapap.2014.03.002] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/01/2014] [Accepted: 03/05/2014] [Indexed: 11/16/2022]
Abstract
The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNA(Pyl). Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate α-amine, and low selectivity toward the anticodon of tRNA(Pyl). These unique but ordinary features of PylRS as an aminoacyl-tRNA synthetase allow the Pyl incorporation machinery to be easily engineered for the genetic incorporation of more than 100 non-canonical amino acids (NCAAs) or α-hydroxy acids into proteins at amber codon and the reassignment of other codons such as ochre UAA, opal UGA, and four-base AGGA codons to code NCAAs.
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Affiliation(s)
- Wei Wan
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA.
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28
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Abstract
Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals (C. elegans and D. melanogaster) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl-transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. Combining chemoselective reactions with encoded amino acids has facilitated the installation of posttranslational modifications, as well as rapid derivatization with diverse fluorophores for imaging.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom;
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29
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Bohlke N, Budisa N. Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. FEMS Microbiol Lett 2014; 351:133-44. [PMID: 24433543 PMCID: PMC4237120 DOI: 10.1111/1574-6968.12371] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering.
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Affiliation(s)
- Nina Bohlke
- Department of Chemistry, TU Berlin, Berlin, Germany
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30
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Chen S, Tsao ML. Genetic Incorporation of a 2-Naphthol Group into Proteins for Site-Specific Azo Coupling. Bioconjug Chem 2013; 24:1645-9. [DOI: 10.1021/bc400168u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shuo Chen
- Chemistry and Chemical Biology
Group, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
| | - Meng-Lin Tsao
- Chemistry and Chemical Biology
Group, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
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31
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Lee YJ, Wu B, Raymond JE, Zeng Y, Fang X, Wooley KL, Liu WR. A genetically encoded acrylamide functionality. ACS Chem Biol 2013; 8:1664-70. [PMID: 23735044 DOI: 10.1021/cb400267m] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nε-Acryloyl-l-lysine, a noncanonical amino acid with an electron deficient olefin, is genetically encoded in Escherichia coli using a pyrrolysyl-tRNA synthetase mutant in coordination with tRNACUAPyl. The acrylamide moiety is stable in cells, whereas it is active enough to perform a diverse set of unique reactions for protein modifications in vitro. These reactions include 1,4-addition, radical polymerization, and 1,3-dipolar cycloaddition. We demonstrate that a protein incorporated with Nε-acryloyl-l-lysine is efficiently modified with thiol-containing nucleophiles at slightly alkali conditions, and the acrylamide moiety also allows rapid radical copolymerization of the same protein into a polyacrylamide hydrogel at physiological pH. At physiological conditions, the acrylamide functionality undergoes a fast 1,3-dipolar cycloaddition reaction with diaryl nitrile imine to show turn-on fluorescence. We have used this observation to demonstrate site-specific fluorescent labeling of proteins incorporated with Nε-acryloyl-l-lysine both in vitro and in living cells. This critical development allows easy access to an array of modified proteins for applications where high specificity and reaction efficiency are needed.
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Affiliation(s)
- Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bo Wu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jeffrey E. Raymond
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xinqiang Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Karen L. Wooley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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32
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Agarwal P, Kudirka R, Albers AE, Barfield RM, de Hart GW, Drake PM, Jones LC, Rabuka D. Hydrazino-Pictet-Spengler ligation as a biocompatible method for the generation of stable protein conjugates. Bioconjug Chem 2013; 24:846-51. [PMID: 23731037 DOI: 10.1021/bc400042a] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aldehyde- and ketone-functionalized biomolecules have found widespread use in biochemical and biotechnological fields. They are typically conjugated with hydrazide or aminooxy nucleophiles under acidic conditions to yield hydrazone or oxime products that are relatively stable, but susceptible to hydrolysis over time. We introduce a new reaction, the hydrazino-Pictet-Spengler (HIPS) ligation, which has two distinct advantages over hydrazone and oxime ligations. First, the HIPS ligation proceeds quickly near neutral pH, allowing for one-step labeling of aldehyde-functionalized proteins under mild conditions. Second, the HIPS ligation product is very stable (>5 days) in human plasma relative to an oxime-linked conjugate (∼1 day), as demonstrated by monitoring protein-fluorophore conjugates by ELISA. Thus, the HIPS ligation exhibits a combination of product stability and speed near neutral pH that is unparalleled by current carbonyl bioconjugation chemistries.
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Affiliation(s)
- Paresh Agarwal
- Redwood Bioscience, 5703 Hollis Street, Emeryville, California 94608, United States
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33
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Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. Multiple Site-Selective Insertions of Noncanonical Amino Acids into Sequence-Repetitive Polypeptides. Chembiochem 2013; 14:968-78. [DOI: 10.1002/cbic.201300069] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/11/2022]
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34
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Odoi KA, Huang Y, Rezenom YH, Liu WR. Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl) pairs in the Escherichia coli BL21(DE3) cell strain. PLoS One 2013; 8:e57035. [PMID: 23520461 PMCID: PMC3592851 DOI: 10.1371/journal.pone.0057035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/16/2013] [Indexed: 12/03/2022] Open
Abstract
Systematic studies of nonsense and sense suppression of the original and three derivative Methanosarcina mazei PylRS-tRNAPyl pairs and cross recognition between nonsense codons and various tRNAPyl anticodons in the Escherichia coli BL21(DE3) cell strain are reported. is orthogonal in E. coli and able to induce strong amber suppression when it is co-expressed with pyrrolysyl-tRNA synthetase (PylRS) and charged with a PylRS substrate, Nε-tert-butoxycarbonyl-l-lysine (BocK). Similar to, is also orthogonal in E. coli and can be coupled with PylRS to genetically incorporate BocK at an ochre mutation site. Although is expected to recognize a UAG codon based on the wobble hypothesis, the PylRS- pair does not give rise to amber suppression that surpasses the basal amber suppression level in E. coli. E. coli itself displays a relatively high opal suppression level and tryptophan (Trp) is incorporated at an opal mutation site. Although the PylRS- pair can be used to encode BocK at an opal codon, the pair fails to suppress the incorporation of Trp at the same site. fails to deliver BocK at an AGG codon when co-expressed with PylRS in E. coli.
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Affiliation(s)
- Keturah A. Odoi
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Ying Huang
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Yohannes H. Rezenom
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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35
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Li Y, Pan M, Li Y, Huang Y, Guo Q. Thiol–yne radical reaction mediated site-specific protein labeling via genetic incorporation of an alkynyl-l-lysine analogue. Org Biomol Chem 2013; 11:2624-9. [DOI: 10.1039/c3ob27116a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Abstract
Aldehyde- and ketone-functionalized proteins are appealing substrates for the development of chemically modified biotherapeutics and protein-based materials. Their reactive carbonyl groups are typically conjugated with α-effect nucleophiles, such as substituted hydrazines and alkoxyamines, to generate hydrazones and oximes, respectively. However, the resulting C=N linkages are susceptible to hydrolysis under physiologically relevant conditions, which limits the utility of such conjugates in biological systems. Here we introduce a Pictet-Spengler ligation that is based on the classic Pictet-Spengler reaction of aldehydes and tryptamine nucleophiles. The ligation exploits the bioorthogonal reaction of aldehydes and alkoxyamines to form an intermediate oxyiminium ion; this intermediate undergoes intramolecular C-C bond formation with an indole nucleophile to form an oxacarboline product that is hydrolytically stable. We used the reaction for site-specific chemical modification of glyoxyl- and formylglycine-functionalized proteins, including an aldehyde-tagged variant of the therapeutic monoclonal antibody Herceptin. In conjunction with techniques for site-specific introduction of aldehydes into proteins, the Pictet-Spengler ligation offers a means to generate stable bioconjugates for medical and materials applications.
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37
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Wu B, Wang Z, Huang Y, Liu WR. Catalyst-free and site-specific one-pot dual-labeling of a protein directed by two genetically incorporated noncanonical amino acids. Chembiochem 2012; 13:1405-8. [PMID: 22628069 DOI: 10.1002/cbic.201200281] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Bo Wu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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38
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Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 2012; 13:168-82. [DOI: 10.1038/nrm3286] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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39
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Neumann H. Rewiring translation - Genetic code expansion and its applications. FEBS Lett 2012; 586:2057-64. [PMID: 22710184 DOI: 10.1016/j.febslet.2012.02.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/02/2012] [Accepted: 02/02/2012] [Indexed: 12/19/2022]
Abstract
With few minor variations, the genetic code is universal to all forms of life on our planet. It is difficult to imagine that one day organisms might exist that use an entirely different code to translate the information of their genome. Recent developments in the field of synthetic biology, however, have opened the gate to their creation. The genetic code of several organisms has been expanded by the heterologous expression of evolved aminoacyl-tRNA synthetase/tRNA(CUA) pairs that mediate the incorporation of unnatural amino acids in response to amber codons. These UAAs introduce exciting new features into proteins, such as spectroscopic probes, UV-inducible crosslinkers, and functional groups for bioorthogonal conjugations or posttranslational modifications. Orthogonal ribosomes provide a parallel translational machinery in Escherichia coli that has lost its evolutionary constraints. Evolved variants of these ribosomes translate amber or quadruplet codons with massively enhanced efficiency. Here, I review these recent developments emphasizing their tremendous potential to facilitate biochemical and cell biological studies.
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Affiliation(s)
- Heinz Neumann
- Institute for Microbiology and Genetics, Justus-von-Liebig Weg 11, Georg-August University Göttingen, 37077 Göttingen, Germany.
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40
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Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 2012; 403:2089-102. [PMID: 22322380 DOI: 10.1007/s00216-012-5784-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/17/2012] [Accepted: 01/23/2012] [Indexed: 02/02/2023]
Abstract
The information used to build proteins is stored in the genetic material of every organism. In nature, ribosomes use 20 native amino acids to synthesize proteins in most circumstances. However, laboratory efforts to expand the genetic repertoire of living cells and organisms have successfully encoded more than 80 nonnative amino acids in E. coli, yeast, and other eukaryotic systems. The selectivity, fidelity, and site-specificity provided by the technology have enabled unprecedented flexibility in manipulating protein sequences and functions in cells. Various biophysical probes can be chemically conjugated or directly incorporated at specific residues in proteins, and corresponding analytical techniques can then be used to answer diverse biological questions. This review summarizes the methodology of genetic code expansion and its recent progress, and discusses the applications of commonly used analytical methods.
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Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol 2012; 23:751-7. [PMID: 22237016 DOI: 10.1016/j.copbio.2011.12.027] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 02/02/2023]
Abstract
The expansion of the genetic code is gradually becoming a core discipline in Synthetic Biology. It offers the best possible platform for the transfer of numerous chemical reactions and processes from the chemical synthetic laboratory into the biochemistry of living cells. The incorporation of biologically occurring or chemically synthesized non-canonical amino acids into recombinant proteins and even proteomes via reprogrammed protein translation is in the heart of these efforts. Orthogonal pairs consisting of aminoacyl-tRNA synthetase and its cognate tRNA proved to be a general tool for the assignment of certain codons of the genetic code with a maximum degree of chemical liberty. Here, we highlight recent developments that should provide a solid basis for the development of generalist tools enabling a controlled variation of chemical composition in proteins and even proteomes. This will take place in the frame of a greatly expanded genetic code with emancipated codons liberated from the current function or with totally new coding units.
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Li Y, Yang M, Huang Y, Song X, Liu L, Chen PR. Genetically encoded alkenyl–pyrrolysine analogues for thiol–ene reaction mediated site-specific protein labeling. Chem Sci 2012. [DOI: 10.1039/c2sc20433a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Hao Z, Hong S, Chen X, Chen PR. Introducing bioorthogonal functionalities into proteins in living cells. Acc Chem Res 2011; 44:742-51. [PMID: 21634380 DOI: 10.1021/ar200067r] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins are the workhorses of the cell, playing crucial roles in virtually every biological process. The revolutionary ability to visualize and monitor proteins in living systems, which is largely the result of the development of green fluorescence protein (GFP) and its derivatives, has dramatically expanded our understanding of protein dynamics and function. Still, GFPs are ill suited in many circumstances; one major drawback is their relatively large size, which can significantly perturb the functions of the native proteins to which they are fused. To bridge this gap, scientists working at the chemistry-biology interface have developed methods to install bioorthogonal functional groups into proteins in living cells. The bioorthogonal group is, by definition, a non-native and nonperturbing chemical group. But more importantly, the installed bioorthogonal handle is able to react with a probe bearing a complementary functionality in a highly selective fashion and with the cell operating in its physiological state. Although extensive efforts have been directed toward the development of bioorthogonal chemical reactions, introducing chemical functionalities into proteins in living systems remains an ongoing challenge. In this Account, we survey recent progress in this area, focusing on a genetic code expansion approach. In nature, a cell uses posttranslational modifications to append the necessary functional groups into proteins that are beyond those contained in the canonical 20 amino acids. Taking lessons from nature, scientists have chosen or engineered certain enzymes to modify target proteins with chemical handles. Alternatively, one can use the cell's translational machinery to genetically encode bioorthogonal functionalities, typically in the form of unnatural amino acids (UAAs), into proteins; this can be done in a residue-specific or a site-specific manner. For studying protein dynamics and function in living cells, site-specific modification by means of genetic code expansion is usually favored. A variety of UAAs bearing bioorthogonal groups as well as other functionalities have been genetically encoded into proteins of interest. Although this approach is well established in bacteria, tagging proteins in mammalian cells is challenging. A facile pyrrolysine-based system, which might potentially become the "one-stop shop" for protein modification in both prokaryotic and eukaryotic cells, has recently emerged. This technology can effectively introduce a series of bioorthogonal handles into proteins in mammalian cells for subsequent chemical conjugation with small-molecule probes. Moreover, the method may provide more precise protein labeling than GFP tagging. These advancements build the foundation for studying more complex cellular processes, such as the dynamics of important receptors on living mammalian cell surfaces.
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Affiliation(s)
- Ziyang Hao
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology, College of Chemistry and Molecular Engineering
| | - Senlian Hong
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology, College of Chemistry and Molecular Engineering
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Chen
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology, College of Chemistry and Molecular Engineering
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences and Department of Chemical Biology, College of Chemistry and Molecular Engineering
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
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Zhang M, Lin S, Song X, Liu J, Fu Y, Ge X, Fu X, Chang Z, Chen PR. A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. Nat Chem Biol 2011; 7:671-7. [DOI: 10.1038/nchembio.644] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 07/05/2011] [Indexed: 12/20/2022]
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Antonczak AK, Morris J, Tippmann EM. Advances in the mechanism and understanding of site-selective noncanonical amino acid incorporation. Curr Opin Struct Biol 2011; 21:481-7. [DOI: 10.1016/j.sbi.2011.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 04/28/2011] [Indexed: 01/01/2023]
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46
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The pyrrolysine translational machinery as a genetic-code expansion tool. Curr Opin Chem Biol 2011; 15:387-91. [PMID: 21507706 DOI: 10.1016/j.cbpa.2011.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 03/14/2011] [Accepted: 03/15/2011] [Indexed: 11/20/2022]
Abstract
The discovery of pyrrolysine not only expanded the set of the known proteinogenic amino acids but also revealed unusual features of its encoding mechanism. The engagement of a canonical stop codon and a unique aminoacyl-tRNA synthetase-tRNA pair that can be used to accommodate a broad range of unnatural amino acids while maintaining strict orthogonality in a variety of prokaryotic and eukaryotic expression systems has proven an invaluable combination. Within a few years since its properties were elucidated, the pyrrolysine translational machinery has become a popular choice for the synthesis of recombinant proteins bearing a wide variety of otherwise hard-to-introduce functional groups. It is also central to the development of new synthetic strategies that rely on stop-codon suppression.
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Yi L, Sun H, Wu YW, Triola G, Waldmann H, Goody RS. A highly efficient strategy for modification of proteins at the C terminus. Angew Chem Int Ed Engl 2011; 49:9417-21. [PMID: 21031382 DOI: 10.1002/anie.201003834] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Long Yi
- Department of Physical Biochemistry, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Hao Z, Song Y, Lin S, Yang M, Liang Y, Wang J, Chen PR. A readily synthesized cyclic pyrrolysine analogue for site-specific protein "click" labeling. Chem Commun (Camb) 2011; 47:4502-4. [PMID: 21387054 DOI: 10.1039/c1cc00024a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A concise route was developed for the facile synthesis of a cyclic pyrrolysine analogue bearing an azide handle. Directed evolution enabled the encoding of this non-natural amino acid in both prokaryotic and eukaryotic cells, which offers a highly efficient approach for the site-specific protein labeling using click chemistry.
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Affiliation(s)
- Ziyang Hao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, China
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Wang YS, Russell WK, Wang Z, Wan W, Dodd LE, Pai PJ, Russell DH, Liu WR. The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of L-phenylalanine and its derivatives. MOLECULAR BIOSYSTEMS 2011; 7:714-7. [PMID: 21234492 DOI: 10.1039/c0mb00217h] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using evolved pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs, L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine have been genetically incorporated into proteins at amber mutation sites in E. coli.
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Affiliation(s)
- Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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50
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Liu WR, Wang YS, Wan W. Synthesis of proteins with defined posttranslational modifications using the genetic noncanonical amino acid incorporation approach. MOLECULAR BIOSYSTEMS 2010; 7:38-47. [PMID: 21088799 DOI: 10.1039/c0mb00216j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranslational modifications modulate the activities of most eukaryotic proteins and play a critical role in all aspects of cellular life. Understanding functional roles of these modifications requires homogeneously modified proteins that are usually difficult to purify from their natural sources. An emerging powerful tool for synthesis of proteins with defined posttranslational modifications is to genetically encode modified amino acids in living cells and incorporate them directly into proteins during the protein translation process. Using this approach, homogenous proteins with tyrosine sulfation, tyrosine phosphorylation mimics, tyrosine nitration, lysine acetylation, lysine methylation, and ubiquitination have been synthesized in large quantities. In this review, we provide a brief introduction to protein posttranslational modifications and the genetic noncanonical amino acid (NAA) incorporation technique, then discuss successful applications of the genetic NAA incorporation approach to produce proteins with defined modifications, and end with challenges and ongoing methodology developments for synthesis of proteins with other modifications.
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Affiliation(s)
- Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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