1
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Kim Y, Cho S, Kim JC, Park HS. tRNA engineering strategies for genetic code expansion. Front Genet 2024; 15:1373250. [PMID: 38516376 PMCID: PMC10954879 DOI: 10.3389/fgene.2024.1373250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs in the translation process and their substantial impact on overall GCE efficiency, ongoing efforts are dedicated to the development of tRNA engineering techniques. This review explores diverse tRNA engineering approaches and provides illustrative examples in the context of GCE, offering insights into the user-friendly implementation of GCE technology.
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Affiliation(s)
| | | | | | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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3
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Synthesis of Fluorescently Labeled Antibodies Using Non-Canonical Amino Acids in Eukaryotic Cell-Free Systems. Methods Mol Biol 2021. [PMID: 33950390 DOI: 10.1007/978-1-0716-1406-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Cell-free protein synthesis (CFPS) enables the development of antibody conjugates, such as fluorophore conjugates and antibody-drug conjugates (ADCs), in a rapid and straightforward manner. In the first part, we describe the cell-free synthesis of antibodies containing fluorescent non-canonical amino acids (ncaa) by using pre-charged tRNA. In the second part, we describe the cell-free synthesis of antibodies containing ncaa by using an orthogonal system, followed by the site-specific conjugation of the fluorescent dye DyLight 650-phosphine. The expression of the antibodies containing ncaa was analyzed by SDS-PAGE, followed by autoradiography and the labeling by in-gel fluorescence. Two different fluorescently labeled antibodies could be generated.
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4
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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5
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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6
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Abstract
Within the broad field of synthetic biology, genetic code expansion (GCE) techniques enable creation of proteins with an expanded set of amino acids. This may be invaluable for applications in therapeutics, bioremediation, and biocatalysis. Central to GCE are aminoacyl-tRNA synthetases (aaRSs) as they link a non-canonical amino acid (ncAA) to their cognate tRNA, allowing ncAA incorporation into proteins on the ribosome. The ncAA-acylating aaRSs and their tRNAs should not cross-react with 20 natural aaRSs and tRNAs in the host, i.e., they need to function as an orthogonal translating system. All current orthogonal aaRS•tRNA pairs have been engineered from naturally occurring molecules to change the aaRS's amino acid specificity or assign the tRNA to a liberated codon of choice. Here we discuss the importance of orthogonality in GCE, laboratory techniques employed to create designer aaRSs and tRNAs, and provide an overview of orthogonal aaRS•tRNA pairs for GCE purposes.
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Affiliation(s)
- Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
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7
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A Combined Cell-Free Protein Synthesis and Fluorescence-Based Approach to Investigate GPCR Binding Properties. Methods Mol Biol 2019; 1947:57-77. [PMID: 30969411 DOI: 10.1007/978-1-4939-9121-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescent labeling of de novo synthesized proteins is in particular a valuable tool for functional and structural studies of membrane proteins. In this context, we present two methods for the site-specific fluorescent labeling of difficult-to-express membrane proteins in combination with cell-free protein synthesis. The cell-free protein synthesis system is based on Chinese Hamster Ovary Cells (CHO) since this system contains endogenous membrane structures derived from the endoplasmic reticulum. These so-called microsomes enable a direct integration of membrane proteins into a biological membrane. In this protocol the first part describes the fluorescent labeling by using a precharged tRNA, loaded with a fluorescent amino acid. The second part describes the preparation of a modified aminoacyl-tRNA-synthetase and a suppressor tRNA that are applied to the CHO cell-free system to enable the incorporation of a non-canonical amino acid. The reactive group of the non-canonical amino acid is further coupled to a fluorescent dye. Both methods utilize the amber stop codon suppression technology. The successful fluorescent labeling of the model G protein-coupled receptor adenosine A2A (Adora2a) is analyzed by in-gel-fluorescence, a reporter protein assay, and confocal laser scanning microscopy (CLSM). Moreover, a ligand-dependent conformational change of the fluorescently labeled Adora2a was analyzed by bioluminescence resonance energy transfer (BRET).
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8
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Huot JL, Shikha S, Schneider A. Inducible orthogonal aminoacylation demonstrates that charging is required for mitochondrial tRNA import in Trypanosoma brucei. Sci Rep 2019; 9:10836. [PMID: 31346230 PMCID: PMC6658472 DOI: 10.1038/s41598-019-47268-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023] Open
Abstract
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs have emerged as powerful means of site-specifically introducing non-standard amino acids into proteins in vivo. Using amino acids with crosslinking moieties this method allows the identification of transient protein-protein interactions. Here we have introduced a previously characterized evolved tyrosyl-tRNA synthetase/suppressor tRNATyr pair from E. coli into the parasitic protozoan Trypanosoma brucei. Upon addition of a suitable non-standard amino acid the suppressor tRNATyr was charged and allowed translation of a green fluorescent protein whose gene contained a nonsense mutation. - T. brucei is unusual in that its mitochondrion lacks tRNA genes indicating that all its organellar tRNAs are imported from the cytosol. Expression of the bacterial tyrosyl-tRNA synthetase in our system is tetracycline-inducible. We have therefore used it to demonstrate that cytosolic aminoacylation of the suppressor tRNATyr induces its import into the mitochondrion.
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Affiliation(s)
- Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.
| | - Shikha Shikha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, CH-3012, Switzerland.
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9
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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10
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Abstract
Expanding the genetic code to enable the incorporation of unnatural amino acids into proteins in biological systems provides a powerful tool for studying protein structure and function. While this technology has been mostly developed and applied in bacterial and mammalian cells, it recently expanded into animals, including worms, fruit flies, zebrafish, and mice. In this review, we highlight recent advances toward the methodology development of genetic code expansion in animal model organisms. We further illustrate the applications, including proteomic labeling in fruit flies and mice and optical control of protein function in mice and zebrafish. We summarize the challenges of unnatural amino acid mutagenesis in animals and the promising directions toward broad application of this emerging technology.
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Affiliation(s)
- Wes Brown
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15237, United States
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15237, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15237, United States
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11
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12
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Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. The central role of tRNA in genetic code expansion. Biochim Biophys Acta Gen Subj 2017; 1861:3001-3008. [PMID: 28323071 DOI: 10.1016/j.bbagen.2017.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins. MAJOR CONCLUSIONS The engineering of orthogonal tRNAs for GCE has significantly improved the incorporation of ncAAs. However, there are numerous unintended consequences of orthogonal tRNA engineering that cannot be predicted ab initio. GENERAL SIGNIFICANCE Genetic code expansion has allowed for the incorporation of a great diversity of ncAAs and novel chemistries into proteins, making significant contributions to our understanding of biological molecules and interactions. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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13
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Incorporation of non-canonical amino acids into proteins in yeast. Fungal Genet Biol 2016; 89:137-156. [DOI: 10.1016/j.fgb.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
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14
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Quast RB, Kortt O, Henkel J, Dondapati SK, Wüstenhagen DA, Stech M, Kubick S. Automated production of functional membrane proteins using eukaryotic cell-free translation systems. J Biotechnol 2015; 203:45-53. [PMID: 25828454 DOI: 10.1016/j.jbiotec.2015.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 12/14/2022]
Abstract
Due to their high abundance and pharmacological relevance there is a growing demand for the efficient production of functional membrane proteins. In this context, cell-free protein synthesis represents a valuable alternative that allows for the high-throughput synthesis of functional membrane proteins. Here, we demonstrate the potential of our cell-free protein synthesis system, based on lysates from cultured Spodoptera frugiperda 21 cells, to produce pro- and eukaryotic membrane proteins with individual topological characteristics in an automated fashion. Analytical techniques, including confocal laser scanning microscopy, fluorescence detection of eYFP fusion proteins in a microplate reader and in-gel fluorescence of statistically incorporated fluorescent amino acid derivatives were employed. The reproducibility of our automated synthesis approach is underlined by coefficients of variation below 7.2%. Moreover, the functionality of the cell-free synthesized potassium channel KcsA was analyzed electrophysiologically. Finally, we expanded our cell-free membrane protein synthesis system by an orthogonal tRNA/synthetase pair for the site-directed incorporation of p-Azido-l-phenylalanine based on stop codon suppression. Incorporation was optimized by performance of a two-dimensional screening with different Mg(2+) and lysate concentrations. Subsequently, the selective modification of membrane proteins with incorporated p-Azido-l-phenylalanine was exemplified by Staudinger ligation with a phosphine-based fluorescence dye.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Oliver Kortt
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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15
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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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16
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Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
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17
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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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18
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Quast RB, Claussnitzer I, Merk H, Kubick S, Gerrits M. Synthesis and site-directed fluorescence labeling of azido proteins using eukaryotic cell-free orthogonal translation systems. Anal Biochem 2014; 451:4-9. [PMID: 24491444 DOI: 10.1016/j.ab.2014.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/17/2014] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
Abstract
Eukaryotic cell-free systems based on wheat germ and Spodoptera frugiperda insect cells were equipped with an orthogonal amber suppressor tRNA-synthetase pair to synthesize proteins with a site-specifically incorporated p-azido-l-phenylalanine residue in order to provide their chemoselective fluorescence labeling with azide-reactive dyes by Staudinger ligation. The specificity of incorporation and bioorthogonality of labeling within complex reaction mixtures was shown by means of translation and fluorescence detection of two model proteins: β-glucuronidase and erythropoietin. The latter contained the azido amino acid in proximity to a signal peptide for membrane translocation into endogenous microsomal vesicles of the insect cell-based system. The results indicate a stoichiometric incorporation of the azido amino acid at the desired position within the proteins. Moreover, the compatibility of cotranslational protein translocation, including glycosylation and amber suppression-based incorporation of p-azido-l-phenylalanine within a cell-free system, is demonstrated. The presented approach should be particularly useful for providing eukaryotic and membrane-associated proteins for investigation by fluorescence-based techniques.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, 14476 Potsdam, Germany
| | | | | | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, 14476 Potsdam, Germany
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19
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Chin JW. Reprogramming the genetic code. EMBO J 2011; 30:2312-24. [PMID: 21602790 PMCID: PMC3116288 DOI: 10.1038/emboj.2011.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 04/27/2011] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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20
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Hino N, Oyama M, Sato A, Mukai T, Iraha F, Hayashi A, Kozuka-Hata H, Yamamoto T, Yokoyama S, Sakamoto K. Genetic Incorporation of a Photo-Crosslinkable Amino Acid Reveals Novel Protein Complexes with GRB2 in Mammalian Cells. J Mol Biol 2011; 406:343-53. [PMID: 21185312 DOI: 10.1016/j.jmb.2010.12.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/06/2010] [Accepted: 12/15/2010] [Indexed: 11/30/2022]
Affiliation(s)
- Nobumasa Hino
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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21
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Thibodeaux GN, Liang X, Moncivais K, Umeda A, Singer O, Alfonta L, Zhang ZJ. Transforming a pair of orthogonal tRNA-aminoacyl-tRNA synthetase from Archaea to function in mammalian cells. PLoS One 2010; 5:e11263. [PMID: 20582317 PMCID: PMC2889833 DOI: 10.1371/journal.pone.0011263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 06/01/2010] [Indexed: 11/19/2022] Open
Abstract
A previously engineered Methanocaldococcus jannaschii tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair orthogonal to Escherichia coli was modified to become orthogonal in mammalian cells. The resulting tRNA(CUA Tyr)-tyrosyl-tRNA synthetase pair was able to suppress an amber codon in the green fluorescent protein, GFP, and in a foldon protein in mammalian cells. The methodology reported here will allow rapid transformation of the much larger collection of existing tyrosyl-tRNA synthetases that were already evolved for the incorporation of an array of over 50 unnatural amino acids into proteins in Escherichia coli into proteins in mammalian cells. Thus we will be able to introduce a large array of possibilities for protein modifications in mammalian cells.
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Affiliation(s)
- Gabrielle Nina Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Xiang Liang
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Kathryn Moncivais
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Aiko Umeda
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
| | - Oded Singer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Lital Alfonta
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (LA); (ZJZ)
| | - Zhiwen Jonathan Zhang
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (LA); (ZJZ)
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22
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23
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Wang Q, Parrish AR, Wang L. Expanding the genetic code for biological studies. CHEMISTRY & BIOLOGY 2009; 16:323-36. [PMID: 19318213 PMCID: PMC2696486 DOI: 10.1016/j.chembiol.2009.03.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 02/25/2009] [Accepted: 03/03/2009] [Indexed: 11/15/2022]
Abstract
Using an orthogonal tRNA-synthetase pair, unnatural amino acids can be genetically encoded with high efficiency and fidelity, and over 40 unnatural amino acids have been site-specifically incorporated into proteins in Escherichia coli, yeast, or mammalian cells. Novel chemical or physical properties embodied in these amino acids enable new means for tailored manipulation of proteins. This review summarizes the methodology and recent progress in expanding this technology to eukaryotic cells. Applications of genetically encoded unnatural amino acids are highlighted with reports on labeling and modifying proteins, probing protein structure and function, identifying and regulating protein activity, and generating proteins with new properties. Genetic incorporation of unnatural amino acids provides a powerful method for investigating a wide variety of biological processes both in vitro and in vivo.
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Affiliation(s)
- Qian Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Angela R. Parrish
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lei Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
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24
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Köhrer C, RajBhandary UL. The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods 2008; 44:129-38. [PMID: 18241794 PMCID: PMC2277081 DOI: 10.1016/j.ymeth.2007.10.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022] Open
Abstract
Here we describe the many applications of acid urea polyacrylamide gel electrophoresis (acid urea PAGE) followed by Northern blot analysis to studies of tRNAs and aminoacyl-tRNA synthetases. Acid urea PAGE allows the electrophoretic separation of different forms of a tRNA, discriminated by changes in bulk, charge, and/or conformation that are brought about by aminoacylation, formylation, or modification of a tRNA. Among the examples described are (i) analysis of the effect of mutations in the Escherichia coli initiator tRNA on its aminoacylation and formylation; (ii) evidence of orthogonality of suppressor tRNAs in mammalian cells and yeast; (iii) analysis of aminoacylation specificity of an archaeal prolyl-tRNA synthetase that can aminoacylate archaeal tRNA(Pro) with cysteine, but does not aminoacylate archaeal tRNA(Cys) with cysteine; (iv) identification and characterization of the AUA-decoding minor tRNA(Ile) in archaea; and (v) evidence that the archaeal minor tRNA(Ile) contains a modified base in the wobble position different from lysidine found in the corresponding eubacterial tRNA.
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MESH Headings
- Amino Acyl-tRNA Synthetases/analysis
- Animals
- Archaea/metabolism
- Blotting, Northern/methods
- Electrophoresis, Polyacrylamide Gel/methods
- Humans
- Hydrogen-Ion Concentration
- Lysine/analogs & derivatives
- Lysine/biosynthesis
- Protein Engineering/methods
- Pyrimidine Nucleosides/biosynthesis
- RNA, Bacterial/isolation & purification
- RNA, Transfer/analysis
- RNA, Transfer/isolation & purification
- RNA, Transfer, Cys/biosynthesis
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Met/metabolism
- Urea
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Affiliation(s)
- Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Wang W, Takimoto JK, Louie GV, Baiga TJ, Noel JP, Lee KF, Slesinger PA, Wang L. Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat Neurosci 2007; 10:1063-72. [PMID: 17603477 PMCID: PMC2692200 DOI: 10.1038/nn1932] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 06/01/2007] [Indexed: 11/09/2022]
Abstract
Proteins participate in various biological processes and can be harnessed to probe and control biological events selectively and reproducibly, but the genetic code limits the building block to 20 common amino acids for protein manipulation in living cells. The genetic encoding of unnatural amino acids will remove this restriction and enable new chemical and physical properties to be precisely introduced into proteins. Here we present new strategies for generating orthogonal tRNA-synthetase pairs, which made possible the genetic encoding of diverse unnatural amino acids in different mammalian cells and primary neurons. Using this new methodology, we incorporated unnatural amino acids with extended side chains into the K+ channel Kv1.4, and found that the bulkiness of residues in the inactivation peptide is essential for fast channel inactivation, a finding that had not been possible using conventional mutagenesis. This technique will stimulate and facilitate new molecular studies using tailored unnatural amino acids for cell biology and neurobiology.
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Affiliation(s)
- Wenyuan Wang
- Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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26
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Abstract
Recently, a general method was developed that makes it possible to genetically encode unnatural amino acids with diverse physical, chemical, or biological properties in Escherichia coli, yeast, and mammalian cells. More than 30 unnatural amino acids have been incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding tRNA/aminoacyl-tRNA synthetase pair. These include fluorescent, glycosylated, metal-ion-binding, and redox-active amino acids, as well as amino acids with unique chemical and photochemical reactivity. This methodology provides a powerful tool both for exploring protein structure and function in vitro and in vivo and for generating proteins with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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27
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Abstract
A general method was recently developed that makes it possible to genetically encode unnatural amino acids (UAAs) with diverse physical, chemical or biological properties in Escherichia coli, yeast, and mammalian cells. Over 30 UAAs have been cotranslationally incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding tRNA-synthetase pair. A key feature of this methodology is the orthogonality between the new translational components and their endogenous host counterparts. Specifically, the codon for the UAA should not encode a common amino acid; neither the new tRNA nor cognate aminoacyl tRNA synthetase should cross-react with any endogenous tRNA-synthetase pairs; and the new synthetase should recognize only the UAA and not any of the 20 common amino acids. This methodology provides a powerful tool for exploring protein structure and function both in vitro and in vivo, as well as generating proteins with new or enhanced properties.
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Affiliation(s)
- Jianming Xie
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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28
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Abstract
More than 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive and redox active amino acids, glycosylated and heavy atom derived amino acids in addition to those with keto, azido and acetylenic chains. In this article, we describe recent advances that make it possible to add new building blocks systematically to the genetic codes of bacteria, yeast and mammalian cells. Taken together these tools will enable the detailed investigation of protein structure and function, which is not possible with conventional mutagenesis. Moreover, by lifting the constraints of the existing 20-amino-acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- T Ashton Cropp
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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29
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30
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Abstract
Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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31
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Chin JW, Cropp TA, Chu S, Meggers E, Schultz PG. Progress toward an expanded eukaryotic genetic code. CHEMISTRY & BIOLOGY 2003; 10:511-9. [PMID: 12837384 DOI: 10.1016/s1074-5521(03)00123-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expanding the eukaryotic genetic code to include unnatural amino acids with novel properties would provide powerful tools for manipulating protein function in eukaryotic cells. Toward this goal, a general approach with potential for isolating aminoacyl-tRNA synthetases that incorporate unnatural amino acids with high fidelity into proteins in Saccharomyces cerevisiae is described. The method is based on activation of GAL4-responsive HIS3, URA3, or lacZ reporter genes by suppression of amber codons in GAL4. The optimization of GAL4 reporters is described, and the positive and negative selection of active Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNA(CUA) is demonstrated. Importantly, both selections can be performed on a single cell and with a range of stringencies. This method will facilitate the isolation of a range of aminoacyl-tRNA synthetase (aaRS)/tRNA(CUA) activities from large libraries of mutant synthetases.
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Affiliation(s)
- Jason W Chin
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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32
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Cleary JD, Mangroo D. Nucleotides of the tRNA D-stem that play an important role in nuclear-tRNA export in Saccharomyces cerevisiae. Biochem J 2000; 347 Pt 1:115-22. [PMID: 10727409 PMCID: PMC1220938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Nuclear export of tRNA in Saccharomyces cerevisiae involves Los1p and Arc1p. Los1p facilitates tRNA translocation across the nuclear pore complex whereas Arc1p plays a role in delivering some species of tRNA exiting the nucleus to their cognate aminoacyl-tRNA synthetases. Here, we show that mutations of C11 and G24 of the D-stem of the yeast tyrosine amber-suppressor tRNA have different effects on nuclear export of the tRNA. Changing G24 had no effect on export of the tRNA to the cytoplasm. In contrast, mutating C11 resulted in nuclear retention of the tRNA. Nuclear retention of the tRNA mutants was not due to lack of processing, since only the mature forms of the tRNA mutants were found. The fact that mutations of G24 did not affect export of the tRNA also indicates that the effect of mutating C11 is not due to gross alteration of the tertiary structure resulting from disruption of the C11/G24 base pair. Expression of Los1p and the mammalian tRNA export receptor exportin-t rescued nuclear export of the tRNA with changes at position 11. The export-defective mutations of the tRNA mutants were suppressed by introducing the complementary nucleotides at position 24. Taken together, these findings suggest that C11 is important for binding of the tRNA to the export receptor, and that this binding is influenced by the conformation of the base. Finally, the export-defective tRNA mutants described can be used as reporters to identify eukaryotic proteins involved in the nuclear-tRNA export process, and characterize the molecular interactions between known receptors and the tRNA substrate.
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MESH Headings
- Base Sequence
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- J D Cleary
- Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry, University of Guelph, Guelph, ON, Canada, N1G 2W1
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Abstract
Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.
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Affiliation(s)
- R Giegé
- Unité Structure des Macromolécules Biologioues et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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Weygand-Durasević I, Nalaskowska M, Söll D. Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli. J Bacteriol 1994; 176:232-9. [PMID: 8282701 PMCID: PMC205035 DOI: 10.1128/jb.176.1.232-239.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In order to gain insight into the conservation of determinants for tRNA identity between organisms, Schizosaccharomyces pombe and human amber suppressor serine tRNA genes have been examined for functional expression in Escherichia coli. The primary transcripts, which originated from E. coli plasmid promoters, were processed into mature tRNAs, but they were poorly aminoacylated in E. coli and thus were nonfunctional as suppressors in vivo. However, coexpression of cloned Saccharomyces cerevisiae seryl-tRNA synthetase led to efficient suppression in E. coli. This shows that some, but not all, determinants specifying the tRNASer identity are conserved in evolution.
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MESH Headings
- Acylation
- Base Sequence
- DNA, Recombinant
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Eukaryotic Cells
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Transfer, Amino Acyl/biosynthesis
- RNA, Transfer, Amino Acyl/isolation & purification
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Schizosaccharomyces/genetics
- Serine-tRNA Ligase/genetics
- Serine-tRNA Ligase/metabolism
- Species Specificity
- Suppression, Genetic
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Affiliation(s)
- I Weygand-Durasević
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
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