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Xu L, Kuan SL, Weil T. Contemporary Approaches for Site-Selective Dual Functionalization of Proteins. Angew Chem Int Ed Engl 2021; 60:13757-13777. [PMID: 33258535 PMCID: PMC8248073 DOI: 10.1002/anie.202012034] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Site-selective protein functionalization serves as an invaluable tool for investigating protein structures and functions in complicated cellular environments and accomplishing semi-synthetic protein conjugates such as traceable therapeutics with improved features. Dual functionalization of proteins allows the incorporation of two different types of functionalities at distinct location(s), which greatly expands the features of native proteins. The attachment and crosstalk of a fluorescence donor and an acceptor dye provides fundamental insights into the folding and structural changes of proteins upon ligand binding in their native cellular environments. Moreover, the combination of drug molecules with different modes of action, imaging agents or stabilizing polymers provides new avenues to design precision protein therapeutics in a reproducible and well-characterizable fashion. This review aims to give a timely overview of the recent advancements and a future perspective of this relatively new research area. First, the chemical toolbox for dual functionalization of proteins is discussed and compared. The strengths and limitations of each strategy are summarized in order to enable readers to select the most appropriate method for their envisaged applications. Thereafter, representative applications of these dual-modified protein bioconjugates benefiting from the synergistic/additive properties of the two synthetic moieties are highlighted.
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Affiliation(s)
- Lujuan Xu
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
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2
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Xu L, Kuan SL, Weil T. Contemporary Approaches for Site‐Selective Dual Functionalization of Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lujuan Xu
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Inorganic Chemistry I Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
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3
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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4
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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5
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Tharp JM, Ad O, Amikura K, Ward FR, Garcia EM, Cate JHD, Schepartz A, Söll D. Initiation of Protein Synthesis with Non‐Canonical Amino Acids In Vivo. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jeffery M. Tharp
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Omer Ad
- Department of Chemistry Yale University New Haven CT 06520 USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Fred R. Ward
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
| | - Emma M. Garcia
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
- Department of Chemistry University of California Berkeley CA 94720 USA
| | - Alanna Schepartz
- Department of Chemistry Yale University New Haven CT 06520 USA
- Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA
- Department of Chemistry University of California Berkeley CA 94720 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA
- Department of Chemistry Yale University New Haven CT 06520 USA
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6
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Tharp JM, Ad O, Amikura K, Ward FR, Garcia EM, Cate JHD, Schepartz A, Söll D. Initiation of Protein Synthesis with Non-Canonical Amino Acids In Vivo. Angew Chem Int Ed Engl 2020; 59:3122-3126. [PMID: 31828898 DOI: 10.1002/anie.201914671] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Indexed: 12/21/2022]
Abstract
By transplanting identity elements into E. coli tRNAfMet , we have engineered an orthogonal initiator tRNA (itRNATy2 ) that is a substrate for Methanocaldococcus jannaschii TyrRS. We demonstrate that itRNATy2 can initiate translation in vivo with aromatic non-canonical amino acids (ncAAs) bearing diverse sidechains. Although the initial system suffered from low yields, deleting redundant copies of tRNAfMet from the genome afforded an E. coli strain in which the efficiency of non-canonical initiation equals elongation. With this improved system we produced a protein containing two distinct ncAAs at the first and second positions, an initial step towards producing completely unnatural polypeptides in vivo. This work provides a valuable tool to synthetic biology and demonstrates remarkable versatility of the E. coli translational machinery for initiation with ncAAs in vivo.
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Affiliation(s)
- Jeffery M Tharp
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Omer Ad
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Fred R Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Emma M Garcia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.,Department of Chemistry, Yale University, New Haven, CT, 06520, USA
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8
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Addy PS, Zheng Y, Italia JS, Chatterjee A. A "Quenchergenic" Chemoselective Protein Labeling Strategy. Chembiochem 2019; 20:1659-1663. [PMID: 30740850 PMCID: PMC6663590 DOI: 10.1002/cbic.201800817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Indexed: 12/21/2022]
Abstract
Dynamic changes in protein structure can be monitored by using a fluorescent probe and a dark quencher. This approach is contingent upon the ability to precisely introduce a fluorophore/quencher pair into two specific sites of a protein of interest. Despite recent advances, there is continued demand for new and convenient approaches to site-selectively label proteins with such optical probes. We have recently developed a chemoselectively rapid azo-coupling reaction (CRACR) for site-specific protein labeling; it relies on rapid coupling between a genetically encoded 5-hydroxytryptophan residue and various aromatic diazonium ions. Herein, it is reported that the product of this conjugation reaction, a highly chromophoric biarylazo group, is a potent fluorescence quencher. The absorption properties of this azo product can be tuned by systematically altering the structure of the aryldiazonium species. A particular "quenchergenic" aryldiazonium has been identified that, upon conjugation, efficiently quenches the fluorescence of green fluorescent protein, which is a widely used genetically encoded fluorescent probe that can be terminally attached to target proteins. This fluorophore/quencher pair was used to evaluate the protein-labeling kinetics of CRACR, as well as to monitor the proteolysis of a fusion protein.
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Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Yunan Zheng
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
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9
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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10
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Musselman CA, Kutateladze TG. Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies. ACS Chem Biol 2019; 14:579-586. [PMID: 30817115 DOI: 10.1021/acschembio.8b01049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Post-translational modifications on histone proteins play critical roles in the regulation of chromatin structure and all DNA-templated processes. Accumulating evidence suggests that these covalent modifications can directly alter chromatin structure, or they can modulate activities of chromatin-modifying and -remodeling factors. Studying these modifications in the context of the nucleosome, the basic subunit of chromatin, is thus of great interest; however, the generation of specifically modified nucleosomes remains challenging. This is especially problematic for most structural biology approaches in which a large amount of material is often needed. Here we discuss the strategies currently available for generation of these substrates. We in particular focus on novel ideas and discuss challenges in the application to structural biology studies.
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Affiliation(s)
- Catherine A. Musselman
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, Iowa 52246, United States
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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11
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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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Chemla Y, Ozer E, Algov I, Alfonta L. Context effects of genetic code expansion by stop codon suppression. Curr Opin Chem Biol 2018; 46:146-155. [DOI: 10.1016/j.cbpa.2018.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/01/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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13
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Yu Y, Hu C, Xia L, Wang J. Artificial Metalloenzyme Design with Unnatural Amino Acids and Non-Native Cofactors. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03754] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yang Yu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Cheng Hu
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lin Xia
- Center
for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Jiangyun Wang
- Laboratory
of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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14
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Ozer E, Chemla Y, Schlesinger O, Aviram HY, Riven I, Haran G, Alfonta L. In vitro suppression of two different stop codons. Biotechnol Bioeng 2016; 114:1065-1073. [DOI: 10.1002/bit.26226] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/22/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Yonatan Chemla
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Orr Schlesinger
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Haim Yuval Aviram
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Inbal Riven
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Gilad Haran
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
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15
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Wang Y, Tsao ML. Reassigning Sense Codon AGA to Encode Noncanonical Amino Acids in Escherichia coli. Chembiochem 2016; 17:2234-2239. [PMID: 27647777 DOI: 10.1002/cbic.201600448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/06/2022]
Abstract
A new method has been developed to reassign the rare codon AGA in Escherichia coli by engineering an orthogonal tRNA/aminoacyl-tRNA synthetase pair derived from Methanocaldococcus jannaschii. The tRNA mutant was introduced with a UCU anticodon, and the synthetase was evolved to correctly recognize the modified tRNA anticodon loop and to selectively charge a target noncanonical amino acid (NAA) onto the tRNA. In order to maximize the efficiency of AGA codon reassignment, while avoiding the lethal effects caused by global codon reassignment in cellular proteins, an inducible promoter (araBAD) was utilized to provide temporal controls for overexpression of the aminoacyl-tRNA synthetase and switch on codon reassignment. Using this system, we were able to efficiently incorporate p-acetylphenylalanine, O-methyl-tyrosine, and p-iodophenylalanine into proteins in response to AGA codons. Also, we found that E. coli strain GM10 was optimal in achieving the highest AGA reassignment rates. The successful reassignment of AGA codons reported here provides a new avenue to further expand the genetic code.
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Affiliation(s)
- Yiyan Wang
- School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
| | - Meng-Lin Tsao
- School of Natural Sciences, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
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16
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Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Duale genetische Kodierung von Acetyllysin und nicht-hydrolysierbarem Thioacetyllysin mittels Flexizym. Angew Chem Int Ed Engl 2016; 128:4151-4154. [DOI: 10.1002/ange.201511750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hai Xiong
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Noah M. Reynolds
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery; Yale University; West Haven CT 06516 USA
| | - Scott J. Miller
- Department of Chemistry; Yale University; 225 Prospect Street New Haven CT 06511 USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry; Yale University; Whitney Avenue 266 New Haven CT 06511 USA
- Department of Chemistry; Yale University; 225 Prospect Street New Haven CT 06511 USA
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17
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Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Dual Genetic Encoding of Acetyl-lysine and Non-deacetylatable Thioacetyl-lysine Mediated by Flexizyme. Angew Chem Int Ed Engl 2016; 55:4083-6. [PMID: 26914285 DOI: 10.1002/anie.201511750] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 11/10/2022]
Abstract
Acetylation of lysine residues is an important post-translational protein modification. Lysine acetylation in histones and its crosstalk with other post-translational modifications in histone and non-histone proteins are crucial to DNA replication, DNA repair, and transcriptional regulation. We incorporated acetyl-lysine (AcK) and the non-hydrolyzable thioacetyl-lysine (ThioAcK) into full-length proteins in vitro, mediated by flexizyme. ThioAcK and AcK were site-specifically incorporated at different lysine positions into human histone H3, either individually or in pairs. We demonstrate that the thioacetyl group in histone H3 could not be removed by the histone deacetylase sirtuin type 1. This method provides a powerful tool to study protein acetylation and its role in crosstalk between post-translational modifications.
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Affiliation(s)
- Hai Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Scott J Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue 266, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
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18
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Friscourt F, Fahrni CJ, Boons GJ. Fluorogenic Strain-Promoted Alkyne-Diazo Cycloadditions. Chemistry 2015; 21:13996-4001. [PMID: 26330090 DOI: 10.1002/chem.201502242] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 01/04/2023]
Abstract
Fluorogenic reactions, in which non- or weakly fluorescent reagents produce highly fluorescent products, are attractive for detecting a broad range of compounds in the fields of bioconjugation and material sciences. Herein, we report that a dibenzocyclooctyne derivative modified with a cyclopropenone moiety (Fl-DIBO) can undergo fast strain-promoted cycloaddition reactions under catalyst-free conditions with azides, nitrones, nitrile oxides, as well as mono- and disubstituted diazo-derivatives. Although the reaction with nitrile oxides, nitrones, and disubstituted diazo compounds gave cycloadducts with low quantum yield, monosubstituted diazo reagents produced 1H-pyrazole derivatives that exhibited an approximately 160-fold fluorescence enhancement over Fl-DIBO combined with a greater than 10,000-fold increase in brightness. Concluding from quantum chemical calculations, fluorescence quenching of 3H-pyrazoles, which are formed by reaction with disubstituted diazo-derivatives, is likely due to the presence of energetically low-lying (n,π*) states. The fluorogenic probe Fl-DIBO was successfully employed for the labeling of diazo-tagged proteins without detectable background signal. Diazo-derivatives are emerging as attractive reporters for the labeling of biomolecules, and the studies presented herein demonstrate that Fl-DIBO can be employed for visualizing such biomolecules without the need for probe washout.
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Affiliation(s)
- Frédéric Friscourt
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA), Fax: (+1) 706-542-4412.,Present address: Institut Européen de Chimie et Biologie, Université de Bordeaux, INCIA, CNRS UMR 5287, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Christoph J Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332 (USA)
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA), Fax: (+1) 706-542-4412.
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Mühlberg M, Hoesl MG, Kuehne C, Dernedde J, Budisa N, Hackenberger CPR. Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds. Beilstein J Org Chem 2015; 11:784-791. [PMID: 26124880 PMCID: PMC4464295 DOI: 10.3762/bjoc.11.88] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/05/2015] [Indexed: 01/12/2023] Open
Abstract
To add new tools to the repertoire of protein-based multivalent scaffold design, we have developed a novel dual-labeling strategy for proteins that combines residue-specific incorporation of unnatural amino acids with chemical oxidative aldehyde formation at the N-terminus of a protein. Our approach relies on the selective introduction of two different functional moieties in a protein by mutually orthogonal copper-catalyzed azide-alkyne cycloaddition (CuAAC) and oxime ligation. This method was applied to the conjugation of biotin and β-linked galactose residues to yield an enzymatically active thermophilic lipase, which revealed specific binding to Erythrina cristagalli lectin by SPR binding studies.
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Affiliation(s)
- Michaela Mühlberg
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 3, 14195 Berlin, Germany
| | - Michael G Hoesl
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian Kuehne
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jens Dernedde
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nediljko Budisa
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian P R Hackenberger
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Institut für Organische und Bioorganische Chemie, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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20
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Hong SH, Kwon YC, Martin RW, Des Soye BJ, de Paz AM, Swonger KN, Ntai I, Kelleher NL, Jewett MC. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. Chembiochem 2015; 16:844-53. [PMID: 25737329 DOI: 10.1002/cbic.201402708] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/12/2022]
Abstract
Site-specific incorporation of non-standard amino acids (NSAAs) into proteins opens the way to novel biological insights and applications in biotechnology. Here, we describe the development of a high yielding cell-free protein synthesis (CFPS) platform for NSAA incorporation from crude extracts of genomically recoded Escherichia coli lacking release factor 1. We used genome engineering to construct synthetic organisms that, upon cell lysis, lead to improved extract performance. We targeted five potential negative effectors to be disabled: the nuclease genes rna, rnb, csdA, mazF, and endA. Using our most productive extract from strain MCJ.559 (csdA(-) endA(-)), we synthesized 550±40 μg mL(-1) of modified superfolder green fluorescent protein containing p-acetyl-L-phenylalanine. This yield was increased to ∼1300 μg mL(-1) when using a semicontinuous method. Our work has implications for using whole genome editing for CFPS strain development, expanding the chemistry of biological systems, and cell-free synthetic biology.
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Affiliation(s)
- Seok Hoon Hong
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208 (USA)
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21
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Al Toma RS, Kuthning A, Exner MP, Denisiuk A, Ziegler J, Budisa N, Süssmuth RD. Site-Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin. Chembiochem 2014; 16:503-9. [DOI: 10.1002/cbic.201402558] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Indexed: 02/01/2023]
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22
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Deepankumar K, Nadarajan SP, Mathew S, Lee SG, Yoo TH, Hong EY, Kim BG, Yun H. Engineering Transaminase for Stability Enhancement and Site-Specific Immobilization through Multiple Noncanonical Amino Acids Incorporation. ChemCatChem 2014. [DOI: 10.1002/cctc.201402882] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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23
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Abstract
Substantial efforts in the past decade have resulted in the systematic expansion of genetic codes, allowing for the direct ribosomal incorporation of ∼100 unnatural amino acids into bacteria, yeast, mammalian cells, and animals. Here, we illustrate the versatility of expanded genetic codes in biology and bioengineering, focusing on the application of expanded genetic codes to problems in protein, cell, synthetic, and experimental evolutionary biology. As the expanded genetic code field continues to develop, its place as a foundational technology in the whole of biological sciences will solidify.
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Affiliation(s)
- Xiang Li
- Department of Biomedical Engineering, University of California at Irvine, 3120 Natural Sciences II, Irvine, CA 92697 (USA)
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24
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Zeng Y, Wang W, Liu WR. Towards reassigning the rare AGG codon in Escherichia coli. Chembiochem 2014; 15:1750-4. [PMID: 25044341 DOI: 10.1002/cbic.201400075] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Indexed: 11/09/2022]
Abstract
The rare AGG codon in Escherichia coli has been reassigned to code non-canonical amino acids (ncAAs) by using the PylRS-tRNA(Pyl)(CCU) pair. When N(ε) -alloc-lysine was used as a PylRS substrate, almost quantitative occupancy of N(ε) -alloc-lysine at an AGG codon site was achieved in minimal medium. ncAAs can be potentially incorporated at the AGG codon with varying efficiencies, depending on their activities towards corresponding enzymes. As AGG is a sense codon, the approach reported here resolves the typical low ncAA incorporation issue that has been associated with ncAA mutagenesis and therefore allows bulk preparation of proteins with site-selectively incorporated ncAAs for applications such as therapeutic protein production.
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Affiliation(s)
- Yu Zeng
- Department of Chemistry, Texas A&M University, College Station, TX 77843 (USA)
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25
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Lammers C, Hahn LE, Neumann H. Optimized plasmid systems for the incorporation of multiple different unnatural amino acids by evolved orthogonal ribosomes. Chembiochem 2014; 15:1800-4. [PMID: 24890611 DOI: 10.1002/cbic.201402033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Indexed: 02/01/2023]
Abstract
Incorporation of multiple different unnatural amino acids into the same polypeptide remains a significant challenge. Orthogonal ribosomes, which are evolvable as they direct the translation of a single dedicated orthogonal mRNA, can provide an avenue to produce such polypeptides routinely. Recent advances in engineering orthogonal ribosomes have created a prototype system to enable genetically encoded introduction of two different functional groups, albeit with limited efficiency. Here, we systematically investigated the limiting factors of this system by using assays to measure the levels and activities of individual components; we identified Methanosarcina barkeri PylRS as a limiting factor for protein yield. Balancing the expression levels of individual components significantly improved growth rate and protein yield. This optimization of the system is likely to increase the scope of evolved orthogonal ribosome-mediated incorporation of multiple different unnatural amino acids.
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Affiliation(s)
- Christoph Lammers
- Free Floater (Junior) Research Group "Applied Synthetic Biology", Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen (Germany)
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26
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Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG. A bacterial strain with a unique quadruplet codon specifying non-native amino acids. Chembiochem 2014; 15:1782-6. [PMID: 24867343 DOI: 10.1002/cbic.201402104] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 02/01/2023]
Abstract
The addition of noncanonical amino acids to the genetic code requires unique codons not assigned to the 20 canonical amino acids. Among the 64 triplet codons, only the three nonsense "stop" codons have been used to encode non-native amino acids. Use of quadruplet "frame-shift" suppressor codons provides an abundant alternative but suffers from low suppression efficiency as a result of competing recognition of their first three bases by endogenous host tRNAs or release factors. Deletion of release factor 1 in a genomically recoded strain of E. coli (E. coli C321), in which all endogenous amber stop codons (UAG) are replaced with UAA, abolished UAG mediated translation termination. Here we show that a Methanocaldococcus jannaschii-derived frame-shift suppressor tRNA/aminoacyl-tRNA synthetase pair enhanced UAGN suppression efficiency in this recoded bacterial strain. These results demonstrate that efficient quadruplet codons for encoding non-native amino acids can be generated by eliminating competing triplet codon recognition at the ribosome.
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Affiliation(s)
- Abhishek Chatterjee
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA); Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467 (USA)
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27
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Nikić I, Plass T, Schraidt O, Szymański J, Briggs JAG, Schultz C, Lemke EA. Minimal Tags for Rapid Dual-Color Live-Cell Labeling and Super-Resolution Microscopy. Angew Chem Int Ed Engl 2014; 53:2245-9. [DOI: 10.1002/anie.201309847] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 12/21/2022]
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28
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Schnelle, zweifarbige Proteinmarkierung an lebenden Zellen für die hochauflösende Mikroskopie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309847] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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29
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Wang XA, Kurra Y, Huang Y, Lee YJ, Liu WR. E1-Catalyzed Ubiquitin C-Terminal Amidation for the Facile Synthesis of Deubiquitinase Substrates. Chembiochem 2013; 15:37-41. [DOI: 10.1002/cbic.201300608] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Indexed: 11/05/2022]
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30
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Xiao H, Chatterjee A, Choi SH, Bajjuri KM, Sinha SC, Schultz PG. Genetic Incorporation of Multiple Unnatural Amino Acids into Proteins in Mammalian Cells. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308137] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Xiao H, Chatterjee A, Choi SH, Bajjuri KM, Sinha SC, Schultz PG. Genetic Incorporation of Multiple Unnatural Amino Acids into Proteins in Mammalian Cells. Angew Chem Int Ed Engl 2013; 52:14080-3. [DOI: 10.1002/anie.201308137] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Indexed: 11/05/2022]
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32
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Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C, Glass JI, Rinehart J, Söll D. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem 2013; 14:1967-72. [PMID: 24000185 DOI: 10.1002/cbic.201300444] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Indexed: 12/22/2022]
Abstract
Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused (or rarely used) codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. The Mycoplasma capricolum genome contains just six CGG arginine codons, without a dedicated tRNA(Arg). We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNA(Pyl)(CCG)), and the genes for pyrrolysine biosynthesis. Here we show that tRNA(Pyl)(CCG) is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of tRNA(Pyl)(CCG), CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 (USA)
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33
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Schmidt MJ, Summerer D. Durch rotes Licht kontrollierte Protein-RNA-Vernetzung mit einem genetisch kodierten Furan. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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34
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Red-Light-Controlled Protein-RNA Crosslinking with a Genetically Encoded Furan. Angew Chem Int Ed Engl 2013; 52:4690-3. [DOI: 10.1002/anie.201300754] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Indexed: 12/12/2022]
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35
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36
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Wu B, Wang Z, Huang Y, Liu WR. Catalyst-free and site-specific one-pot dual-labeling of a protein directed by two genetically incorporated noncanonical amino acids. Chembiochem 2012; 13:1405-8. [PMID: 22628069 DOI: 10.1002/cbic.201200281] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Bo Wu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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37
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Hoesl MG, Budisa N. In Vivo Incorporation of Multiple Noncanonical Amino Acids into Proteins. Angew Chem Int Ed Engl 2011; 50:2896-902. [DOI: 10.1002/anie.201005680] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 11/11/2022]
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38
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Hoesl MG, Budisa N. Paralleler In-vivo-Einbau von mehreren nichtkanonischen Aminosäuren in Proteine. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005680] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Hoesl MG, Budisa N. Expanding and Engineering the Genetic Code in a Single Expression Experiment. Chembiochem 2011; 12:552-5. [DOI: 10.1002/cbic.201000586] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 12/31/2022]
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40
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Ayyadurai N, Deepankumar K, Prabhu NS, Lee S, Yun H. A facile and efficient method for the incorporation of multiple unnatural amino acids into a single protein. Chem Commun (Camb) 2011; 47:3430-2. [DOI: 10.1039/c0cc04672h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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42
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Lepthien S, Merkel L, Budisa N. Doppelte und dreifache In-vivo-Funktionalisierung von Proteinen mit synthetischen Aminosäuren. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000439] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Lepthien S, Merkel L, Budisa N. In Vivo Double and Triple Labeling of Proteins Using Synthetic Amino Acids. Angew Chem Int Ed Engl 2010; 49:5446-50. [DOI: 10.1002/anie.201000439] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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