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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Lu W, Terasaka N, Sakaguchi Y, Suzuki T, Suzuki T, Suga H. An anticodon-sensing T-boxzyme generates the elongator nonproteinogenic aminoacyl-tRNA in situ of a custom-made translation system for incorporation. Nucleic Acids Res 2024; 52:3938-3949. [PMID: 38477328 DOI: 10.1093/nar/gkae151] [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: 11/21/2023] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
In the hypothetical RNA world, ribozymes could have acted as modern aminoacyl-tRNA synthetases (ARSs) to charge tRNAs, thus giving rise to the peptide synthesis along with the evolution of a primitive translation apparatus. We previously reported a T-boxzyme, Tx2.1, which selectively charges initiator tRNA with N-biotinyl-phenylalanine (BioPhe) in situ in a Flexible In-vitro Translation (FIT) system to produce BioPhe-initiating peptides. Here, we performed in vitro selection of elongation-capable T-boxzymes (elT-boxzymes), using para-azido-l-phenylalanine (PheAZ) as an acyl-donor. We implemented a new strategy to enrich elT-boxzyme-tRNA conjugates that self-aminoacylated on the 3'-terminus selectively. One of them, elT32, can charge PheAZ onto tRNA in trans in response to its cognate anticodon. Further evolution of elT32 resulted in elT49, with enhanced aminoacylation activity. We have demonstrated the translation of a PheAZ-containing peptide in an elT-boxzyme-integrated FIT system, revealing that elT-boxzymes are able to generate the PheAZ-tRNA in response to the cognate anticodon in situ of a custom-made translation system. This study, together with Tx2.1, illustrates a scenario where a series of ribozymes could have overseen aminoacylation and co-evolved with a primitive RNA-based translation system.
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Affiliation(s)
- Wei Lu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Medical Biochemistry, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0125, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, 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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3
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Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 PMCID: PMC11151186 DOI: 10.1021/jacs.3c11306] [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: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
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Affiliation(s)
- Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joshua E. Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Eugene N. Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
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4
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Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
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Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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5
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Wu Y, Bertran MT, Joshi D, Maslen SL, Hurd C, Walport LJ. Identification of photocrosslinking peptide ligands by mRNA display. Commun Chem 2023; 6:103. [PMID: 37258712 PMCID: PMC10232439 DOI: 10.1038/s42004-023-00898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Catherine Hurd
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.
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6
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Chan AI, Sawant MS, Burdick DJ, Tom J, Song A, Cunningham CN. Evaluating Translational Efficiency of Noncanonical Amino Acids to Inform the Design of Druglike Peptide Libraries. ACS Chem Biol 2023; 18:81-90. [PMID: 36607609 PMCID: PMC9872084 DOI: 10.1021/acschembio.2c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Advances in genetic code reprogramming have allowed the site-specific incorporation of noncanonical functionalities into polypeptides and proteins, providing access to wide swaths of chemical space via in vitro translation techniques like mRNA display. Prior efforts have established that the translation machinery can tolerate amino acids with modifications to both the peptide backbone and side chains, greatly broadening the chemical space that can be interrogated in ligand discovery efforts. However, existing methods for confirming the translation yield of new amino acid building blocks for these technologies necessitate multistep workups and, more importantly, are not relevant for measuring translation within the context of a combinatorial library consisting of multiple noncanonical amino acids. In this study, we developed a luminescence-based assay to rapidly assess the relative translation yield of any noncanonical amino acid in real time. Among the 59 amino acids tested here, we found that many translate with high efficiency, but translational yield is not necessarily correlated to whether the amino acid is proteinogenic or has high tRNA acylation efficiency. Interestingly, we found that single-template translation data can inform the library-scale translation yield and that shorter peptide libraries are more tolerant of lower-efficiency amino acid monomers. Together our data show that the luminescence-based assay described herein is an essential tool in evaluating new building blocks and codon table designs within mRNA display toward the goal of developing druglike peptide-based libraries for drug discovery campaigns.
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Affiliation(s)
- Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Manali S. Sawant
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Daniel J. Burdick
- Department
of Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Jeffrey Tom
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Aimin Song
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States,
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7
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Katoh T, Suga H. In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids. Annu Rev Biochem 2022; 91:221-243. [PMID: 35729073 DOI: 10.1146/annurev-biochem-040320-103817] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic code reprogramming has enabled us to ribosomally incorporate various nonproteinogenic amino acids (npAAs) into peptides in vitro. The repertoire of usable npAAs has been expanded to include not only l-α-amino acids with noncanonical sidechains but also those with noncanonical backbones. Despite successful single incorporation of npAAs, multiple and consecutive incorporations often suffer from low efficiency or are even unsuccessful. To overcome this stumbling block, engineering approaches have been used to modify ribosomes, EF-Tu, and tRNAs. Here, we provide an overview of these in vitro methods that are aimed at optimal expansion of the npAA repertoire and their applications for the development of de novo bioactive peptides containing various npAAs.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
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8
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Hecht SM. Expansion of the Genetic Code Through the Use of Modified Bacterial Ribosomes. J Mol Biol 2022; 434:167211. [PMID: 34419431 PMCID: PMC9990327 DOI: 10.1016/j.jmb.2021.167211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Biological protein synthesis is mediated by the ribosome, and employs ~20 proteinogenic amino acids as building blocks. Through the use of misacylated tRNAs, presently accessible by any of several strategies, it is now possible to employ in vitro and in vivo protein biosynthesis to elaborate proteins containing a much larger variety of amino acid building blocks. However, the incorporation of this broader variety of amino acids is limited to those species utilized by the ribosome. As a consequence, virtually all of the substrates utilized over time have been L-α-amino acids. In recent years, a variety of structural and biochemical studies have provided important insights into those regions of the 23S ribosomal RNA that are involved in peptide bond formation. Subsequent experiments, involving the randomization of key regions of 23S rRNA required for peptide bond formation, have afforded libraries of E. coli harboring plasmids with the rrnB gene modified in the key regions. Selections based on the use of modified puromycin derivatives with altered amino acids then identified clones uniquely sensitive to individual puromycin derivatives. These clones often recognized misacylated tRNAs containing altered amino acids similar to those in the modified puromycins, and incorporated the amino acid analogues into proteins. In this fashion, it has been possible to realize the synthesis of proteins containing D-amino acids, β-amino acids, phosphorylated amino acids, as well as long chain and cyclic amino acids in which the nucleophilic amino group is not in the α-position. Of special interest have been dipeptides and dipeptidomimetics of diverse utility.
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Affiliation(s)
- Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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9
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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10
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Gamper H, Hou YM. A Label-Free Assay for Aminoacylation of tRNA. Genes (Basel) 2020; 11:genes11101173. [PMID: 33036365 PMCID: PMC7601589 DOI: 10.3390/genes11101173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022] Open
Abstract
Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the rate of cell growth. Traditional assays for the quantification of tRNA aminoacylation involve radioactivity, either with a radioactive amino acid or with a [3′-32P]-labeled tRNA. We describe here a label-free assay that monitors aminoacylation by biotinylation-streptavidin (SA) conjugation to the α-amine or the α-imine of the aminoacyl group on the aa-tRNA. The conjugated aa-tRNA product is readily separated from the unreacted tRNA by a denaturing polyacrylamide gel, allowing for quantitative measurement of aminoacylation. This label-free assay is applicable to a wide range of amino acids and tRNA sequences and to both classes of aminoacylation. It is more sensitive and robust than the assay with a radioactive amino acid and has the potential to explore a wider range of tRNA than the assay with a [3′-32P]-labeled tRNA. This label-free assay reports kinetic parameters of aminoacylation quantitatively similar to those reported by using a radioactive amino acid, suggesting its broad applicability to research relevant to human health and disease.
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11
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Wang T, Liang C, Xu H, An Y, Xiao S, Zheng M, Liu L, Nie L. Incorporation of nonstandard amino acids into proteins: principles and applications. World J Microbiol Biotechnol 2020; 36:60. [PMID: 32266578 DOI: 10.1007/s11274-020-02837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 01/01/2023]
Abstract
The cellular ribosome shows a naturally evolved strong preference for the synthesis of proteins with standard amino acids. An in-depth understanding of the translation process enables scientists to go beyond this natural limitation and engineer translating systems capable of synthesizing proteins with artificially designed and synthesized non-standard amino acids (nsAA) featuring more bulky sidechains. The sidechains can be functional groups, with chosen biophysical or chemical activities, that enable the direct application of these proteins. Alternatively, the sidechains can be designed to contain highly reactive groups: enabling the ready formation of conjugates via a covalent bond between the sidechain and other chemicals or biomolecules. This co-translational incorporation of nsAAs into proteins allows for a vast number of possible applications. In this paper, we first systematically summarized the advances in the engineering of the translation system. Subsequently, we reviewed the extensive applications of these nsAA-containing proteins (after chemical modification) by discussing representative reports on how they can be utilized for different purposes. Finally, we discussed the direction of further studies which could be undertaken to improve the current technology utilized in incorporating nsAAs in order to use them to their full potential and improve accessibility across disciplines.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Hongjv Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yafei An
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Sha Xiao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Mengyuan Zheng
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lu Liu
- College of International Education, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Lei Nie
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, Henan, China.
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12
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Tsiamantas C, Kwon S, Rogers JM, Douat C, Huc I, Suga H. Ribosomal Incorporation of Aromatic Oligoamides as Peptide Sidechain Appendages. Angew Chem Int Ed Engl 2020; 59:4860-4864. [PMID: 31894626 PMCID: PMC7496375 DOI: 10.1002/anie.201914654] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/24/2019] [Indexed: 01/06/2023]
Abstract
Derivatives of 4-aminomethyl-l-phenylalanine with aromatic oligoamide foldamers as sidechain appendages were successfully charged on tRNA by means of flexizymes. Their subsequent incorporation both at the C-terminus of, and within, peptide sequences by the ribosome, was demonstrated. These results expand the registry of chemical structures tolerated by the ribosome to sidechains significantly larger and more structurally defined than previously demonstrated.
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Affiliation(s)
- Christos Tsiamantas
- Department of ChemistrySchool of ScienceThe University of Tokyo7-3-1 HongoBunkyoTokyo113-0033Japan
| | - Sunbum Kwon
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
- Department of ChemistryChung-Ang University84 Heukseok-roDongjak-guSeoul06974Republic of Korea
| | - Joseph M. Rogers
- Department of ChemistrySchool of ScienceThe University of Tokyo7-3-1 HongoBunkyoTokyo113-0033Japan
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of Tokyo7-3-1 HongoBunkyoTokyo113-0033Japan
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13
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Tsiamantas C, Kwon S, Rogers JM, Douat C, Huc I, Suga H. Ribosomal Incorporation of Aromatic Oligoamides as Peptide Sidechain Appendages. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christos Tsiamantas
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Sunbum Kwon
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
- Department of ChemistryChung-Ang University 84 Heukseok-ro Dongjak-gu Seoul 06974 Republic of Korea
| | - Joseph M. Rogers
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
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14
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Nigro G, Bourcier S, Lazennec-Schurdevin C, Schmitt E, Marlière P, Mechulam Y. Use of β 3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase. J Struct Biol 2019; 209:107435. [PMID: 31862305 DOI: 10.1016/j.jsb.2019.107435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/15/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022]
Abstract
Polypeptides containing β-amino acids are attractive tools for the design of novel proteins having unique properties of medical or industrial interest. Incorporation of β-amino acids in vivo requires the development of efficient aminoacyl-tRNA synthetases specific of these non-canonical amino acids. Here, we have performed a detailed structural and biochemical study of the recognition and use of β3-Met by Escherichia coli methionyl-tRNA synthetase (MetRS). We show that MetRS binds β3-Met with a 24-fold lower affinity but catalyzes the esterification of the non-canonical amino acid onto tRNA with a rate lowered by three orders of magnitude. Accurate measurements of the catalytic parameters required careful consideration of the presence of contaminating α-Met in β3-Met commercial samples. The 1.45 Å crystal structure of the MetRS: β3-Met complex shows that β3-Met binds the enzyme essentially like α-Met, but the carboxylate moiety is mobile and not adequately positioned to react with ATP for aminoacyl adenylate formation. This study provides structural and biochemical bases for engineering MetRS with improved β3-Met aminoacylation capabilities.
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Affiliation(s)
- Giuliano Nigro
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Sophie Bourcier
- Laboratoire de Chimie Moléculaire, LCM, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.
| | - Philippe Marlière
- Xenome Research Group, Institute of Systems and Synthetic Biology, CNRS, UMR8030, UEVE, CEA, GENOPOLE, 5 rue Henri Desbruères, 91030 Evry Cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.
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15
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Yin Y, Ochi N, Craven TW, Baker D, Takigawa N, Suga H. De Novo Carborane-Containing Macrocyclic Peptides Targeting Human Epidermal Growth Factor Receptor. J Am Chem Soc 2019; 141:19193-19197. [PMID: 31752491 DOI: 10.1021/jacs.9b09106] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
l-Carboranylalanine (LCba) is a unique artificial amino acid containing a cluster of 10 boron atoms. Since the three-dimensional aromaticity and charge distributions of the carborane side chain are quite different from any side chains of proteinogenic amino acids, there is no report whether LCba can be a substrate for the translation machinery. Here, we report studies on the ribosomal incorporation of LCba into peptide via initiation and elongation using the flexizyme-assisted translation system. Our results indicate that only the initiation step could tolerate LCba incorporation, but the elongation steps could not, very likely due to its steric bulkiness of the side chain. Based on this knowledge, we have designed a library of macrocyclic peptides initiated by α-N-(2-choloroacetyl)-l-carboranylalanine (ClAc-LCba) and selected molecules capable of binding to human epidermal growth factor receptor (hEGFR). Two peptides that were forwarded to deeper studies exhibited affinities with KD values at 16 and 20 nM against hEGFR. Computational modeling of one of the peptides suggested that the carborane side chain might be directly involved in the interaction with the hydrophobic β-sheet core in the EGF binding site of hEGFR, which is consistent with the mutational data where replacing LCba residue with LPhe completely eliminated the binding activity. Cell lines that stably express hEGFR could be stained by incubation with the C-terminal fluorescein-labeled peptides, whereas hEGFR-negative cells could not be stained. This study provides a general strategy for the de novo discovery of carborane-containing macrocyclic peptides targeting various tumor biomarker proteins, potentially applicable to boron neutron capture therapy.
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Affiliation(s)
- Yizhen Yin
- Department of Chemistry, School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo , Tokyo 113-0033 , Japan
| | - Nobuaki Ochi
- Department of General Internal Medicine 4 , Kawasaki Medical School , 2-6-1 Nakasange , Kita-ku , Okayama 700-8505 , Japan
| | - Timothy W Craven
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - David Baker
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Nagio Takigawa
- Department of General Internal Medicine 4 , Kawasaki Medical School , 2-6-1 Nakasange , Kita-ku , Okayama 700-8505 , Japan
| | - Hiroaki Suga
- Department of Chemistry, School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo , Tokyo 113-0033 , Japan
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16
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Fujino T, Kondo T, Suga H, Murakami H. Exploring the Minimal RNA Substrate of Flexizymes. Chembiochem 2019; 20:1959-1965. [PMID: 30950544 DOI: 10.1002/cbic.201900150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 02/06/2023]
Abstract
Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogues. However, their minimal RNA substrate has not been investigated. Here we have designed fluorescently labeled short RNAs corresponding to the four, three, and two bases (4bRNA, 3bRNA, 2bRNA) at the tRNA 3'-end and explored the minimal RNA substrate of flexizymes, dFx and eFx. 3bRNA was the observed minimal RNA substrate of the flexizymes, but the efficiency of acylation of this short RNA was two to three times lower than that of 4bRNA. The efficiency of acylation of 4bRNA was comparable with that of the microhelix, a 22-base RNA conventionally used as a tRNA analogue for analyzing acylation efficiency. We also compared the efficiencies of acylation of the microhelix and 4bRNA with various acid substrates. Thanks to the short length of 4bRNA, its acyl-4bRNA products exhibited larger mobility shifts in gel electrophoresis than those exhibited by acyl-microhelix products with every substrate tested. This indicated that 4bRNA was an ideal RNA substrate for analyzing the efficiency of acylation by flexizymes.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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17
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Tsiamantas C, Otero-Ramirez ME, Suga H. Discovery of Functional Macrocyclic Peptides by Means of the RaPID System. Methods Mol Biol 2019; 2001:299-315. [PMID: 31134577 DOI: 10.1007/978-1-4939-9504-2_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flexizymes, highly flexible tRNA aminoacylation ribozymes, have enabled charging of virtually any amino acid (including non-proteogenic ones) onto tRNA molecules. Coupling to a custom-made in vitro translation system, namely the flexible in vitro translation (FIT) system, has unveiled the remarkable tolerance of the ribosome toward molecules, remote from what nature has selected to carry out its elaborate functions. Among the very diverse molecules and chemistries that have been ribosomally incorporated, a plethora of entities capable of mediating intramolecular cyclization have revolutionized the design and discovery of macrocyclic peptides. These macrocyclization reactions (which can be spontaneous, chemical, or enzymatic) have all served as tools for the discovery of peptides with natural-like structures and properties. Coupling of the FIT system and mRNA display techniques, known as the random non-standard peptide integrated discovery (RaPID) system, has in turn allowed for the simultaneous screening of trillions of macrocyclic peptides against challenging biological targets. The macrocyclization methodologies are chosen depending on the structural and functional characteristics of the desired molecule. Thus, they can emanate from the peptide's N-terminus or its side chains, attributing flexibility or rigidity, or even result in the installation of fluorescent probes.
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Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Manuel E Otero-Ramirez
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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18
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Gamper H, Hou YM. tRNA 3'-amino-tailing for stable amino acid attachment. RNA (NEW YORK, N.Y.) 2018; 24:1878-1885. [PMID: 30217865 PMCID: PMC6239183 DOI: 10.1261/rna.068015.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Amino acids are attached to the tRNA 3'-end as a prerequisite for entering the ribosome for protein synthesis. Amino acid attachment also gives tRNA access to nonribosomal cellular activities. However, the normal attachment is via an ester linkage between the carboxylic group of the amino acid and the 3'-hydroxyl of the terminal A76 ribose in tRNA. The instability of this ester linkage has severely hampered studies of aminoacyl-tRNAs. Although the use of 3'-amino-3'-deoxy A76 in a 3'-amino-tailed tRNA provides stable aminoacyl attachment via an amide linkage, there are multiple tailing protocols and the efficiency of each relative to the others is unknown. Here we compare five different tailing protocols in parallel, all dependent on the CCA-adding enzyme [CTP(ATP): tRNA nucleotidyl transferase; abbreviated as the CCA enzyme] to exchange the natural ribose with the modified one. We show that the most efficient protocol is achieved by the CCA-catalyzed pyrophosphorolysis removal of the natural A76 in equilibrium with the addition of the appropriate ATP analog to synthesize the modified 3'-end. This protocol for 3'-amino-tailing affords quantitative and stable attachment of a broad range of amino acids to tRNA, indicating its general utility for studies of aminoacyl-tRNAs in both canonical and noncanonical activities.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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19
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Huang Y, Wiedmann MM, Suga H. RNA Display Methods for the Discovery of Bioactive Macrocycles. Chem Rev 2018; 119:10360-10391. [PMID: 30395448 DOI: 10.1021/acs.chemrev.8b00430] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The past two decades have witnessed the emergence of macrocycles, including macrocyclic peptides, as a promising yet underexploited class of de novo drug candidates. Both rational/computational design and in vitro display systems have contributed tremendously to the development of cyclic peptide binders of either traditional targets such as cell-surface receptors and enzymes or challenging targets such as protein-protein interaction surfaces. mRNA display, a key platform technology for the discovery of cyclic peptide ligands, has become one of the leading strategies that can generate natural-product-like macrocyclic peptide binders with antibody-like affinities. On the basis of the original cell-free transcription/translation system, mRNA display is highly evolvable to realize its full potential by applying genetic reprogramming and chemical/enzymatic modifications. In addition, mRNA display also allows the follow-up hit-to-lead development using high-throughput focused affinity maturation. Finally, mRNA-displayed peptides can be readily engineered to create chemical conjugates based on known small molecules or biologics. This review covers the birth and growth of mRNA display and discusses the above features of mRNA display with success stories and future perspectives and is up to date as of August 2018.
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Affiliation(s)
- Yichao Huang
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Mareike Margarete Wiedmann
- 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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20
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Passioura T, Suga H. A RaPID way to discover nonstandard macrocyclic peptide modulators of drug targets. Chem Commun (Camb) 2018; 53:1931-1940. [PMID: 28091672 DOI: 10.1039/c6cc06951g] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues. Using this technique, it is possible to synthesise peptides containing a range of structural features (macrocyclic backbones, backbone N-methylation, d-stereochemistry, etc.) commonly observed in natural product secondary metabolites, a chemical class that has historically been a rich source of drug-like molecules. Moreover, when combined with biochemical display screening technologies, this synthetic approach can be used to generate (and screen for target affinity) extremely diverse (in excess of 1012 compound) chemical libraries, making it an extraordinary tool for drug discovery. The current review charts the history of flexizyme technology and its use for non-canonical peptide synthesis and screening.
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Affiliation(s)
- Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan. and Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), Saitama 332-0012, Japan
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21
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Suga H. Max-Bergmann award lecture:A RaPID way to discover bioactive nonstandard peptides assisted by the flexizyme and FIT systems. J Pept Sci 2018; 24. [PMID: 29322648 DOI: 10.1002/psc.3055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022]
Abstract
Although general review articles should cover various people's achievements related to the subject, this review is privileged to describe the technology developed by Suga (and colleagues) as a recipient of the Max-Bergmann Medal in 2016. The technology consists of 3 unique and essential tools, flexizymes, FIT, and RaPID systems. This review describes the history of the development of each tool and discusses the recent applications of the RaPID system to discover potent nonstandard peptides for therapeutic and diagnostic uses.
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Affiliation(s)
- Hiroaki Suga
- Department of Chemistry, Graduate School of Science, Tokyo, The University of Tokyo, Japan
- JST-CREST, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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22
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Habibi L, Salmani H. Pivotal Impacts of Retrotransposon Based Invasive RNAs on Evolution. Front Microbiol 2017; 8:1957. [PMID: 29067016 PMCID: PMC5641331 DOI: 10.3389/fmicb.2017.01957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/22/2017] [Indexed: 11/16/2022] Open
Abstract
RNAs have long been described as the mediators of gene expression; they play a vital role in the structure and function of cellular complexes. Although the role of RNAs in the prokaryotes is mainly confined to these basic functions, the effects of these molecules in regulating the gene expression and enzymatic activities have been discovered in eukaryotes. Recently, a high-resolution analysis of the DNA obtained from different organisms has revealed a fundamental impact of the RNAs in shaping the genomes, heterochromatin formation, and gene creation. Deep sequencing of the human genome revealed that about half of our DNA is comprised of repetitive sequences (remnants of transposable element movements) expanded mostly through RNA-mediated processes. ORF2 encoded by L1 retrotransposons is a cellular reverse transcriptase which is mainly responsible for RNA invasion of various transposable elements (L1s, Alus, and SVAs) and cellular mRNAs in to the genomic DNA. In addition to increasing retroelements copy number; genomic expansion in association with centromere, telomere, and heterochromatin formation as well as pseudogene creation are the evolutionary consequences of this RNA-based activity. Threatening DNA integrity by disrupting the genes and forming excessive double strand breaks is another effect of this invasion. Therefore, repressive mechanisms have been evolved to control the activities of these invasive intracellular RNAs. All these mechanisms now have essential roles in the complex cellular functions. Therefore, it can be concluded that without direct action of RNA networks in shaping the genome and in the development of different cellular mechanisms, the evolution of higher eukaryotes would not be possible.
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Abstract
In ribosomal translation, only 20 kinds of proteinogenic amino acids (pAAs), namely 19 l-amino acids and glycine, are exclusively incorporated into polypeptide chain. To overcome this limitation, various methods to introduce non-proteinogenic amino acids (npAAs) other than the 20 pAAs have been developed to date. However, the repertoire of amino acids that can be simultaneously introduced is still limited. Moreover, the efficiency of npAA incorporation is not always sufficient depending on their structures. Fidelity of translation is sometimes low due to misincorporation of competing pAAs and/or undesired translation termination. Here, we provide an overview of efforts to solve these issues, focusing on the engineering of tRNAs.
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Affiliation(s)
- Takayuki Katoh
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan.,b JST, PRESTO , 7-3-1 Hongo, Bunkyo-ku , Tokyo , Japan
| | - Yoshihiko Iwane
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan
| | - Hiroaki Suga
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo , Japan.,c JST, CREST , 7-3-1 Hongo, Bunkyo-ku , Tokyo , Japan
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25
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Abstract
Understanding how life arose is a fundamental problem of biology. Much progress has been made by adopting a synthetic and mechanistic perspective on originating life. We present a current view of the biochemistry of the origin of life, focusing on issues surrounding the emergence of an RNA World in which RNA dominated informational and functional roles. There is cause for optimism on this difficult problem: the prebiotic chemical inventory may not have been as nightmarishly complex as previously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of self-replicating RNA; encapsulation in protocells provides evolutionary and biophysical advantages. Nevertheless, major issues remain unsolved, such as the origin of a genetic code. Attention to this field is particularly timely given the accelerating discovery and characterization of exoplanets.
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Fujino T, Goto Y, Suga H, Murakami H. Ribosomal Synthesis of Peptides with Multiple β-Amino Acids. J Am Chem Soc 2016; 138:1962-9. [DOI: 10.1021/jacs.5b12482] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomoshige Fujino
- Department
of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hiroshi Murakami
- Department
of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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27
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Ogawa A, Namba Y, Gakumasawa M. Rational optimization of amber suppressor tRNAs toward efficient incorporation of a non-natural amino acid into protein in a eukaryotic wheat germ extract. Org Biomol Chem 2016; 14:2671-8. [DOI: 10.1039/c5ob02533h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Amber suppressor tRNAs (sup-tRNAs) were rationally optimized toward efficient incorporation of a non-natural amino acid (AcPhe) into protein in a eukaryotic wheat germ extract.
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Affiliation(s)
| | - Yuki Namba
- Proteo-Science Center
- Ehime University
- Matsuyama
- Japan
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28
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Rogers JM, Suga H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org Biomol Chem 2015; 13:9353-63. [PMID: 26280393 DOI: 10.1039/c5ob01336d] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
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Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
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29
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Terasaka N, Iwane Y, Geiermann AS, Goto Y, Suga H. Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides. Int J Mol Sci 2015; 16:6513-31. [PMID: 25803109 PMCID: PMC4394545 DOI: 10.3390/ijms16036513] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/03/2022] Open
Abstract
Genetic code expansion and reprogramming methodologies allow us to incorporate non-canonical amino acids (ncAAs) bearing various functional groups, such as fluorescent groups, bioorthogonal functional groups, and post-translational modifications, into a desired position or multiple positions in polypeptides both in vitro and in vivo. In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS)–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. In this review we summarize recent advances in the field of ribosomal polypeptide synthesis containing ncAAs.
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Affiliation(s)
- Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshihiko Iwane
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Anna-Skrollan Geiermann
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Ogawa A, Doi Y. Investigation of end processing and degradation of premature tRNAs and their application to stabilization of in vitro transcripts in wheat germ extract. Org Biomol Chem 2015; 13:1008-12. [DOI: 10.1039/c4ob02221a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the end processing and degradation of premature tRNAs in wheat germ extract (left), which led to the findings of end protectors for efficiently stabilizing an in vitro transcript (purple, right).
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Affiliation(s)
| | - Yasunori Doi
- Proteo-Science Center
- Ehime University
- Matsuyama
- Japan
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31
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Passioura T, Suga H. Reprogramming the genetic code in vitro. Trends Biochem Sci 2014; 39:400-8. [DOI: 10.1016/j.tibs.2014.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 02/07/2023]
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Xu J, Appel B, Balke D, Wichert C, Müller S. RNA aminoacylation mediated by sequential action of two ribozymes and a nonactivated amino acid. Chembiochem 2014; 15:1200-9. [PMID: 24764272 DOI: 10.1002/cbic.201300741] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Indexed: 01/29/2023]
Abstract
In the transition from the RNA world to the modern DNA/protein world, RNA-catalyzed aminoacylation might have been a key step towards early translation. A number of ribozymes capable of aminoacylating their own 3' termini have been developed by in vitro selection. However, all of those catalysts require a previously activated amino acid-typically an aminoacyl-AMP-as substrate. Here we present two ribozymes connected by intermolecular base pairing and carrying out the two steps of aminoacylation: ribozyme 1 loads nonactivated phenylalanine onto its phosphorylated 5' terminus, thereby forming a high-energy mixed anhydride. Thereafter, a complex of ribozymes 1 and 2 is formed by intermolecular base pairing, and the "activated" phenylalanine is transferred from the 5' terminus of ribozyme 1 to the 3' terminus of ribozyme 2. This kind of simple RNA aminoacylase complex was engineered from previously selected ribozymes possessing the two required activities. RNA aminoacylation with a nonactivated amino acid as described here is advantageous to RNA world scenarios because initial amino acid activation by an additional reagent (in most cases, ATP) and an additional ribozyme would not be necessary.
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Affiliation(s)
- Jiacui Xu
- Ernst Moritz Arndt Universität Greifswald, Institut für Biochemie, Felix Hausdorff Strasse 4, 17487 Greifswald (Germany); Current address: Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706 (USA)
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Generation and selection of ribozyme variants with potential application in protein engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3389-99. [DOI: 10.1007/s00253-014-5528-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 12/22/2022]
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Das M, Vargas-Rodriguez O, Goto Y, Suga H, Musier-Forsyth K. Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation. Nucleic Acids Res 2013; 42:3943-53. [PMID: 24371276 PMCID: PMC3973320 DOI: 10.1093/nar/gkt1332] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Errors in protein synthesis due to mispairing of amino acids with tRNAs jeopardize cell viability. Several checkpoints to prevent formation of Ala- and Cys-tRNAPro have been described, including the Ala-specific editing domain (INS) of most bacterial prolyl-tRNA synthetases (ProRSs) and an autonomous single-domain INS homolog, YbaK, which clears Cys-tRNAPro in trans. In many species where ProRS lacks an INS domain, ProXp-ala, another single-domain INS-like protein, is responsible for editing Ala-tRNAPro. Although the amino acid specificity of these editing domains has been established, the role of tRNA sequence elements in substrate selection has not been investigated in detail. Critical recognition elements for aminoacylation by bacterial ProRS include acceptor stem elements G72/A73 and anticodon bases G35/G36. Here, we show that ProXp-ala and INS require these same acceptor stem and anticodon elements, respectively, whereas YbaK lacks inherent tRNA specificity. Thus, these three related domains use divergent approaches to recognize tRNAs and prevent mistranslation. Whereas some editing domains have borrowed aspects of tRNA recognition from the parent aminoacyl-tRNA synthetase, relaxed tRNA specificity leading to semi-promiscuous editing may offer advantages to cells.
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Affiliation(s)
- Mom Das
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA and Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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35
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Hipolito CJ, Tanaka Y, Katoh T, Nureki O, Suga H. A macrocyclic peptide that serves as a cocrystallization ligand and inhibits the function of a MATE family transporter. Molecules 2013; 18:10514-30. [PMID: 23999725 PMCID: PMC6270235 DOI: 10.3390/molecules180910514] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/24/2013] [Accepted: 08/27/2013] [Indexed: 11/29/2022] Open
Abstract
The random non-standard peptide integrated discovery (RaPID) system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound extrusion (PfMATE) transporter and inhibit the transport function. Moreover, these macrocyclic peptides were successfully employed as cocrystallization ligands of selenomethionine-labeled PfMATE. In this report, we disclose the details of the RaPID selection strategy that led to the identification of these three macrocyclic peptides as well as a fourth macrocyclic peptide, MaD8, which is exclusively discussed in this article. MaD8 was found to bind within the cleft of PfMATE’s extracellular side and blocked the path of organic small molecules being extruded. The results of an ethidium bromide efflux assay confirmed the efflux inhibitory activity of MaD8, whose behavior was similar to that of previously reported MaD5.
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Affiliation(s)
- Christopher J. Hipolito
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
| | - Yoshiki Tanaka
- Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Authors to whom correspondence should be addressed; E-Mails: (O.N.); (H.S.); Tel./Fax: +81-3-5841-8372 (H.S)
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan; E-Mails: (C.J.H.); (T.K.)
- Authors to whom correspondence should be addressed; E-Mails: (O.N.); (H.S.); Tel./Fax: +81-3-5841-8372 (H.S)
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Lee KB, Kim HC, Kim DM, Kang TJ, Suga H. Comparative evaluation of two cell-free protein synthesis systems derived from Escherichia coli for genetic code reprogramming. J Biotechnol 2013; 164:330-5. [PMID: 23395618 DOI: 10.1016/j.jbiotec.2013.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/11/2013] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
Abstract
Genetic codes can be reprogrammed to code for non-proteinogenic amino acids during protein synthesis. Technologically, these non-proteinogenic amino acids are incorporated into proteins by artificially charging them to suppressor-tRNAs that can reprogram the existing codons. Several methods and systems for genetic code reprogramming have been reported including methods for charging non-proteinogenic amino acids to tRNA molecules, codons for reprogramming, and systems for protein synthesis. However, there has been no systematic, comparative evaluation of cell-free protein synthesis systems in genetic code reprogramming for their efficiencies and robustness even with their potential usefulness in the field. Here we compare two cell-free protein synthesis systems, the crude S12 and PURE system, with the codon systems, non-proteinogenic amino acids, and the positions in the protein for reprogramming as variables. We show that the combined use of CCCG four-nucleotide codon that is newly developed in this study and the crude S12 system is the most reliable and robust method of choice, while the use of traditional UAG amber stop codon along with an RNA aptamer toward peptide release factor 1 can yield the most plentiful product with certain variations.
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Affiliation(s)
- Ki Baek Lee
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul, Republic of Korea.
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Suga H, Hayashi G, Terasaka N. The RNA origin of transfer RNA aminoacylation and beyond. Philos Trans R Soc Lond B Biol Sci 2012; 366:2959-64. [PMID: 21930588 DOI: 10.1098/rstb.2011.0137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacylation of tRNA is an essential event in the translation system. Although in the modern system protein enzymes play the sole role in tRNA aminoacylation, in the primitive translation system RNA molecules could have catalysed aminoacylation onto tRNA or tRNA-like molecules. Even though such RNA enzymes so far are not identified from known organisms, in vitro selection has generated such RNA catalysts from a pool of random RNA sequences. Among them, a set of RNA sequences, referred to as flexizymes (Fxs), discovered in our laboratory are able to charge amino acids onto tRNAs. Significantly, Fxs allow us to charge a wide variety of amino acids, including those that are non-proteinogenic, onto tRNAs bearing any desired anticodons, and thus enable us to reprogramme the genetic code at our will. This article summarizes the evolutionary history of Fxs and also the most recent advances in manipulating a translation system by integration with Fxs.
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Affiliation(s)
- Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan.
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38
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Hayashi G, Goto Y, Suga H. Ribosome Evolution for Two Artificial Amino Acids in E. coli. ACTA ACUST UNITED AC 2010; 17:320-1. [DOI: 10.1016/j.chembiol.2010.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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40
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Wohlgemuth I, Brenner S, Beringer M, Rodnina MV. Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem 2008; 283:32229-35. [PMID: 18809677 DOI: 10.1074/jbc.m805316200] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosome catalyzes peptide bond formation between peptidyl-tRNA in the P site and aminoacyl-tRNA in the A site. Here, we show that the nature of the C-terminal amino acid residue in the P-site peptidyl-tRNA strongly affects the rate of peptidyl transfer. Depending on the C-terminal amino acid of the peptidyl-tRNA, the rate of reaction with the small A-site substrate puromycin varied between 100 and 0.14 s(-1), regardless of the tRNA identity. The reactivity decreased in the order Lys = Arg > Ala > Ser > Phe = Val > Asp >> Pro, with Pro being by far the slowest. However, when Phe-tRNA(Phe) was used as A-site substrate, the rate of peptide bond formation with any peptidyl-tRNA was approximately 7 s(-1), which corresponds to the rate of binding of Phe-tRNA(Phe) to the A site (accommodation). Because accommodation is rate-limiting for peptide bond formation, the reaction rate is uniform for all peptidyl-tRNAs, regardless of the variations of the intrinsic chemical reactivities. On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation.
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Affiliation(s)
- Ingo Wohlgemuth
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
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41
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Goto Y, Murakami H, Suga H. Initiating translation with D-amino acids. RNA (NEW YORK, N.Y.) 2008; 14:1390-8. [PMID: 18515548 PMCID: PMC2441986 DOI: 10.1261/rna.1020708] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/30/2008] [Indexed: 05/19/2023]
Abstract
Here we report experimental evidence that the translation initiation apparatus accepts D-amino acids ((D)aa), as opposed to only L-methionine, as initiators. Nineteen (D)aa, as the stereoisomers to their natural L-amino acids, were charged onto initiator tRNA(fMet)(CAU) using flexizyme technology and tested for initiation in a reconstituted Escherichia coli translation system lacking methionine, i.e., the initiator was reprogrammed from methionine to (D)aa. Remarkably, all (D)aa could initiate translation while the efficiency of initiation depends upon the type of side chain. The peptide product initiated with (D)aa was generally in a nonformylated form, indicating that methionyl-tRNA formyltransferase poorly formylated the corresponding (D)aa-tRNA(fMet)(CAU). Although the inefficient formylation of (D)aa-tRNA(fMet)(CAU) resulted in modest expression of the corresponding peptide, preacetylation of (D)aa-tRNA(fMet)(CAU) dramatically increased expression level, implying that the formylation efficiency is one of the critical determinants of initiation efficiency with (D)aa. Our findings provide not only the experimental evidence that translation initiation tolerates (D)aa, but also a new means for the mRNA-directed synthesis of peptides capped with (D)aa or acyl-(D)aa at the N terminus.
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Affiliation(s)
- Yuki Goto
- Research Center of Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
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42
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Ohta A, Yamagishi Y, Suga H. Synthesis of biopolymers using genetic code reprogramming. Curr Opin Chem Biol 2008; 12:159-67. [PMID: 18249198 DOI: 10.1016/j.cbpa.2007.12.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 12/27/2007] [Indexed: 11/25/2022]
Abstract
Genetic code reprogramming is a new emerging methodology that enables us to synthesize non-standard peptides containing multiple non-proteinogenic amino acids using translation machinery. This review describes the historical background of this methodology and what distinguishes it from the classical 'nonsense suppression' methodology, followed by a discussion of recent developments in combining this methodology with other compatible technologies. Specifically, we discuss in detail the combination of genetic code reprogramming with flexizymes, de novo tRNA acylation ribozymes that facilitate the charging process of a variety of non-proteinogenic amino acids onto tRNAs bearing designated anticodons, and summarize some of the recent demonstrations of the synthesis of non-standard peptides with cyclic structure or/and altered backbones employing this technology.
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Affiliation(s)
- Atsushi Ohta
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan
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43
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Goto Y, Ohta A, Sako Y, Yamagishi Y, Murakami H, Suga H. Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem Biol 2008; 3:120-9. [PMID: 18215017 DOI: 10.1021/cb700233t] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The initiation codon dictates that the translation initiation event exclusively begins with methionine. We report here a new technology to reprogram the initiation event, where various amino acids and those bearing N (alpha)-acyl groups can be used as an initiator for peptide synthesis. The technology is built upon the concept of genetic code reprogramming, where methionine is depleted from the translation system and the initiation codon is reassigned to the desired amino acid. We have applied this technology to the synthesis of an antitumor cyclic peptide, G7-18NATE, closed by a physiologically stable bond, and it is also extended to the custom synthesis of its analogues with various ring sizes. Significantly, cyclization occurs spontaneously upon translation of the precursor linear peptides. To demonstrate the practicality of this methodology, we also prepared a small cyclic peptide library designated by 160 distinct mRNAs. Thus, this technology offers a new means to prepare a wide array of in vivo compatible cyclic peptide libraries for the discovery of peptidic drug candidates against various therapeutic targets.
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Affiliation(s)
- Yuki Goto
- Research Center for Advanced
Science and Technology
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering
| | - Atsushi Ohta
- Research Center for Advanced
Science and Technology
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
| | - Yusuke Sako
- Research Center for Advanced
Science and Technology
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
| | - Yusuke Yamagishi
- Research Center for Advanced
Science and Technology
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
| | | | - Hiroaki Suga
- Research Center for Advanced
Science and Technology
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
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Splan KE, Musier-Forsyth K, Boniecki MT, Martinis SA. In vitro assays for the determination of aminoacyl-tRNA synthetase editing activity. Methods 2008; 44:119-28. [PMID: 18241793 PMCID: PMC2270698 DOI: 10.1016/j.ymeth.2007.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 10/29/2007] [Indexed: 11/21/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes that help to ensure the fidelity of protein translation by accurately aminoacylating (or "charging") specific tRNA substrates with cognate amino acids. Many synthetases have an additional catalytic activity to confer amino acid editing or proofreading. This activity relieves ambiguities during translation of the genetic code that result from one synthetase activating multiple amino acid substrates. In this review, we describe methods that have been developed for assaying both pre- and post-transfer editing activities. Pre-transfer editing is defined as hydrolysis of a misactivated aminoacyl-adenylate prior to transfer to the tRNA. This reaction has been reported to occur either in the aminoacylation active site or in a separate editing domain. Post-transfer editing refers to the hydrolysis reaction that cleaves the aminoacyl-ester linkage formed between the carbonyl carbon of the amino acid and the 2' or 3' hydroxyl group of the ribose on the terminal adenosine. Post-transfer editing takes place in a hydrolytic active site that is distinct from the site of amino acid activation. Here, we focus on methods for determination of steady-state reaction rates using editing assays developed for both classes of synthetases.
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Affiliation(s)
- Kathryn E Splan
- Department of Chemistry, Macalester College, St. Paul, MN 55105, USA
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45
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Kawakami T, Murakami H, Suga H. Messenger RNA-Programmed Incorporation of Multiple N-Methyl-Amino Acids into Linear and Cyclic Peptides. ACTA ACUST UNITED AC 2008; 15:32-42. [DOI: 10.1016/j.chembiol.2007.12.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 11/25/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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46
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Ohta A, Murakami H, Higashimura E, Suga H. Synthesis of Polyester by Means of Genetic Code Reprogramming. ACTA ACUST UNITED AC 2007; 14:1315-22. [DOI: 10.1016/j.chembiol.2007.10.015] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 09/11/2007] [Accepted: 10/22/2007] [Indexed: 11/28/2022]
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Rodriguez EA, Lester HA, Dougherty DA. Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 1: minimizing misacylation. RNA (NEW YORK, N.Y.) 2007; 13:1703-14. [PMID: 17698638 PMCID: PMC1986802 DOI: 10.1261/rna.666807] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The incorporation of unnatural amino acids site-specifically is a valuable technique for structure-function studies, incorporation of biophysical probes, and determining protein-protein interactions. THG73 is an amber suppressor tRNA used extensively for the incorporation of >100 different residues in over 20 proteins, but under certain conditions THG73 is aminoacylated in vivo by endogenous aminoacyl-tRNA synthetase. Similar aminoacylation is seen with the Escherichia coli Asn amber suppressor tRNA, which has also been used to incorporate UAAs in many studies. We now find that the natural amino acid placed on THG73 is Gln. Since the E. coli GlnRS recognizes positions in the acceptor stem, we made several acceptor stem mutations in the second to fourth positions on THG73. All mutations reduce aminoacylation in vivo and allow for the selection of highly orthogonal tRNAs. To show the generality of these mutations, we created opal suppressor tRNAs that show less aminoacylation in Xenopus oocytes relative to THG73. We have created a library of Tetrahymena thermophila Gln amber suppressor tRNAs that will be useful for determining optimal suppressor tRNAs for use in other eukaryotic cells.
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Affiliation(s)
- Erik A Rodriguez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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48
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Rodriguez EA, Lester HA, Dougherty DA. Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 2: evaluating suppression efficiency. RNA (NEW YORK, N.Y.) 2007; 13:1715-22. [PMID: 17698637 PMCID: PMC1986817 DOI: 10.1261/rna.667607] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The incorporation of unnatural amino acids into proteins is a valuable tool for addition of biophysical probes, bio-orthogonal functionalities, and photoreactive cross-linking agents, although these approaches often require quantities of protein that are difficult to access with chemically aminoacylated tRNAs. THG73 is an amber suppressor tRNA that has been used extensively, incorporating over 100 residues in 20 proteins. In vitro studies have shown that the Escherichia coli Asn amber suppressor (ENAS) suppresses better than THG73. However, we report here that ENAS suppresses with <26% of the efficiency of THG73 in Xenopus oocytes. We then tested the newly developed Tetrahymena thermophila Gln amber suppressor (TQAS) tRNA library, which contains mutations in the second to fourth positions of the acceptor stem. The acceptor stem mutations have no adverse effect on suppression efficiency and, in fact, can increase the suppression efficiency. Combining mutations causes an averaging of suppression efficiency, and increased suppression efficiency does not correlate with increased DeltaG of the acceptor stem. We created a T. thermophila opal suppressor, TQOpS', which shows approximately 50% suppression efficiency relative to THG73. The TQAS tRNA library, composed of functional suppressor tRNAs, has been created and will allow for screening in eukaryotic cells, where rapid analysis of large libraries is not feasible.
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Affiliation(s)
- Erik A Rodriguez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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49
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Ohuchi M, Murakami H, Suga H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr Opin Chem Biol 2007; 11:537-42. [PMID: 17884697 DOI: 10.1016/j.cbpa.2007.08.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 08/05/2007] [Accepted: 08/06/2007] [Indexed: 11/17/2022]
Abstract
Flexizymes are de novo ribozymes capable of charging a wide variety of non-natural amino acids on tRNAs. The flexizyme system enables reprogramming of the genetic code by reassigning the codons that are generally assigned to natural amino acids to non-natural residues, and thus mRNA-directed synthesis of non-natural polypeptides can be achieved. In this review, we comprehensively summarize the history of the flexizyme system and its subsequent development into a practical tool. Furthermore, applications to the synthesis of novel biopolymers via genetic code reprogramming and perspectives for future applications are described.
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Affiliation(s)
- Masaki Ohuchi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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50
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Ueno S, Arai H, Suzuki M, Husimi Y. An mRNA-protein fusion at N-terminus for evolutionary protein engineering. Int J Biol Sci 2007; 3:365-74. [PMID: 17848981 PMCID: PMC1975775 DOI: 10.7150/ijbs.3.365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Accepted: 08/27/2007] [Indexed: 11/26/2022] Open
Abstract
A novel method to link a nascent protein (phenotype) to its mRNA (genotype) covalently through the N-terminus was developed. The mRNA harboring amber stop codon at just downstream of initiation site was hybridized with hydrazide-modified ssDNA at upstream of coding region and was ligated to the DNA. This construct was then modified with 4-acetyl-phenylalanyl amber suppressor tRNA. This modified construct was fused with the nascent protein via the phenylalanine derivative when the mRNA uses the amber suppressor tRNA to decode the amber stop codon. The obtained fusion molecule was used successfully in selective enrichment experiments. It will be applicable for high-through-put screening in evolutionary protein engineering. In contrast to fusion molecules generated by other methods in which the protein is linked to genotype molecule through the C- terminus, our fusion molecule will serve to select a protein for which the C-terminus is essential to be active.
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Affiliation(s)
- Shingo Ueno
- Department of Functional Materials Science, Saitama University, Shimo-okubo, Sakura-ku, Saitama, Japan
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