101
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Affiliation(s)
- Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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102
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Abstract
Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.
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Affiliation(s)
- Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616-8665 Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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103
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Soye BJD, Patel JR, Isaacs FJ, Jewett MC. Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol 2015; 28:83-90. [PMID: 26186264 DOI: 10.1016/j.cbpa.2015.06.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
The translation system (the ribosome and associated factors) is the cell's factory for protein synthesis. The extraordinary catalytic capacity of the protein synthesis machinery has driven extensive efforts to harness it for novel functions. For example, pioneering efforts have demonstrated that it is possible to genetically encode more than the 20 natural amino acids and that this encoding can be a powerful tool to expand the chemical diversity of proteins. Here, we discuss recent advances in efforts to expand the chemistry of living systems, highlighting improvements to the molecular machinery and genomically recoded organisms, applications of cell-free systems, and extensions of these efforts to include eukaryotic systems. The transformative potential of repurposing the translation apparatus has emerged as one of the defining opportunities at the interface of chemical and synthetic biology.
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Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jaymin R Patel
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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104
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Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni HR, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N. Chemische Evolution eines bakteriellen Proteoms. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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105
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Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N, Haruki M, Kohashi S, Yamagishi K, Murayama K, Tomabechi Y, Itagaki T, Akasaka R, Kawazoe M, Takemoto C, Shirouzu M, Yokoyama S, Sakamoto K. Protein stabilization utilizing a redefined codon. Sci Rep 2015; 5:9762. [PMID: 25985257 PMCID: PMC4434908 DOI: 10.1038/srep09762] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/18/2015] [Indexed: 12/30/2022] Open
Abstract
Recent advances have fundamentally changed the ways in which synthetic amino acids are incorporated into proteins, enabling their efficient and multiple-site incorporation, in addition to the 20 canonical amino acids. This development provides opportunities for fresh approaches toward addressing fundamental problems in bioengineering. In the present study, we showed that the structural stability of proteins can be enhanced by integrating bulky halogenated amino acids at multiple selected sites. Glutathione S-transferase was thus stabilized significantly (by 5.2 and 5.6 kcal/mol) with 3-chloro- and 3-bromo-l-tyrosines, respectively, incorporated at seven selected sites. X-ray crystallographic analyses revealed that the bulky halogen moieties filled internal spaces within the molecules, and formed non-canonical stabilizing interactions with the neighboring residues. This new mechanism for protein stabilization is quite simple and applicable to a wide range of proteins, as demonstrated by the rapid stabilization of the industrially relevant azoreductase.
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Affiliation(s)
- Kazumasa Ohtake
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Atsushi Yamaguchi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takahito Mukai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroki Kashimura
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Nobutaka Hirano
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Mitsuru Haruki
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Sosuke Kohashi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kenji Yamagishi
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
| | - Kazutaka Murayama
- Biomedical Engineering Research Organization, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Itagaki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ryogo Akasaka
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Masahito Kawazoe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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106
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Quast RB, Mrusek D, Hoffmeister C, Sonnabend A, Kubick S. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. FEBS Lett 2015; 589:1703-12. [PMID: 25937125 DOI: 10.1016/j.febslet.2015.04.041] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Devid Mrusek
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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107
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Lewis JC. Metallopeptide catalysts and artificial metalloenzymes containing unnatural amino acids. Curr Opin Chem Biol 2015; 25:27-35. [PMID: 25545848 PMCID: PMC4380757 DOI: 10.1016/j.cbpa.2014.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/03/2014] [Accepted: 12/11/2014] [Indexed: 01/24/2023]
Abstract
Metallopeptide catalysts and artificial metalloenzymes built from peptide scaffolds and catalytically active metal centers possess a number of exciting properties that could be exploited for selective catalysis. Control over metal catalyst secondary coordination spheres, compatibility with library based methods for optimization and evolution, and biocompatibility stand out in this regard. A wide range of unnatural amino acids (UAAs) have been incorporated into peptide and protein scaffolds using several distinct methods, and the resulting UAAs containing scaffolds can be used to create novel hybrid metal-peptide catalysts. Promising levels of selectivity have been demonstrated for several hybrid catalysts, and these provide a strong impetus and important lessons for the design of and optimization of hybrid catalysts.
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Affiliation(s)
- Jared C Lewis
- University of Chicago, Department of Chemistry, 5735 South Ellis Avenue, Chicago, IL 60637, United States.
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108
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Cui Z, Stein V, Tnimov Z, Mureev S, Alexandrov K. Semisynthetic tRNA complement mediates in vitro protein synthesis. J Am Chem Soc 2015; 137:4404-13. [PMID: 25822136 DOI: 10.1021/ja5131963] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Genetic code expansion is a key objective of synthetic biology and protein engineering. Most efforts in this direction are focused on reassigning termination or decoding quadruplet codons. While the redundancy of genetic code provides a large number of potentially reassignable codons, their utility is diminished by the inevitable interaction with cognate aminoacyl-tRNAs. To address this problem, we sought to establish an in vitro protein synthesis system with a simplified synthetic tRNA complement, thereby orthogonalizing some of the sense codons. This quantitative in vitro peptide synthesis assay allowed us to analyze the ability of synthetic tRNAs to decode all of 61 sense codons. We observed that, with the exception of isoacceptors for Asn, Glu, and Ile, the majority of 48 synthetic Escherichia coli tRNAs could support protein translation in the cell-free system. We purified to homogeneity functional Asn, Glu, and Ile tRNAs from the native E. coli tRNA mixture, and by combining them with synthetic tRNAs, we formulated a semisynthetic tRNA complement for all 20 amino acids. We further demonstrated that this tRNA complement could restore the protein translation activity of tRNA-depleted E. coli lysate to a level comparable to that of total native tRNA. To confirm that the developed system could efficiently synthesize long polypeptides, we expressed three different sequences coding for superfolder GFP. This novel semisynthetic translation system is a powerful tool for tRNA engineering and potentially enables the reassignment of at least 9 sense codons coding for Ser, Arg, Leu, Pro, Thr, and Gly.
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Affiliation(s)
- Zhenling Cui
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Viktor Stein
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zakir Tnimov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience and the Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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109
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Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Recoded organisms engineered to depend on synthetic amino acids. Nature 2015; 518:89-93. [PMID: 25607356 PMCID: PMC4590768 DOI: 10.1038/nature14095] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/17/2014] [Indexed: 01/21/2023]
Abstract
Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels, and chemicals1. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs in open systems2,3, which include bioremediation4 and probiotics5. Although safeguards have been designed to control cell growth by essential gene regulation6, inducible toxin switches7, and engineered auxotrophies8, these approaches are compromised by cross-feeding of essential metabolites, leaked expression of essential genes, or genetic mutations9,10. Here, we describe the construction of a series of genomically recoded organisms (GROs)11 whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). We introduced a Methanocaldococcus jannaschii tRNA:aminoacyl-tRNA synthetase (aaRS) pair into the chromosome of a GRO that lacks all TAG codons and release factor 1, endowing this organism with the orthogonal translational components to convert TAG into a dedicated sense codon for sAAs. Using multiplex automated genome engineering (MAGE)12, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids. Of the 60 sAA-dependent variants isolated, a notable strain harboring 3 TAG codons in conserved functional residues13 of MurG, DnaA and SerS and containing targeted tRNA deletions maintained robust growth and exhibited undetectable escape frequencies upon culturing ∼1011 cells on solid media for seven days or in liquid media for 20 days. This is a significant improvement over existing biocontainment approaches2,3,6-10. We constructed synthetic auxotrophs dependent on sAAs that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternate genetic codes that impart genetic isolation by impeding horizontal gene transfer11 and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.
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Affiliation(s)
- Alexis J Rovner
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Adrian D Haimovich
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Spencer R Katz
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Zhe Li
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Michael W Grome
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Brandon M Gassaway
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Miriam Amiram
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jaymin R Patel
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Ryan R Gallagher
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jesse Rinehart
- 1] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA [2] Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520, USA
| | - Farren J Isaacs
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Systems Biology Institute, Yale University, West Haven, Connecticut 06516, USA
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110
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Hadd A, Perona JJ. Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering. ACS Chem Biol 2014; 9:2761-6. [PMID: 25310879 PMCID: PMC4273986 DOI: 10.1021/cb5006596] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
have taken a rational approach to redesigning the amino acid
binding and aminoacyl–tRNA pairing specificities of bacterial
glutaminyl–tRNA synthetase. The four-stage engineering incorporates
generalizable design principles and improves the pairing efficiency
of noncognate glutamate with tRNAGln by over 105-fold compared to the wild-type enzyme. Better optimized designs
of the protein–RNA complex include substantial reengineering
of the globular core region of the tRNA, demonstrating a role for
specific tRNA nucleotides in specifying the identity of the genetically
encoded amino acid. Principles emerging from this engineering effort
open new prospects for combining rational and genetic selection approaches
to design novel aminoacyl–tRNA synthetases that ligate noncanonical
amino acids onto tRNAs. This will facilitate reconstruction of the
cellular translation apparatus for applications in synthetic biology.
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Affiliation(s)
- Andrew Hadd
- Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - John J. Perona
- Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
- Department
of Chemistry, Portland State University, PO Box 751, Portland, Oregon 97207, United States
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111
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Bullwinkle T, Lazazzera B, Ibba M. Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic Code. Annu Rev Genet 2014; 48:149-66. [DOI: 10.1146/annurev-genet-120213-092101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tammy Bullwinkle
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Beth Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
- Ohio State Biochemistry Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210;
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112
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113
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Reducing the genetic code induces massive rearrangement of the proteome. Proc Natl Acad Sci U S A 2014; 111:17206-11. [PMID: 25404328 DOI: 10.1073/pnas.1420193111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Expanding the genetic code is an important aim of synthetic biology, but some organisms developed naturally expanded genetic codes long ago over the course of evolution. Less than 1% of all sequenced genomes encode an operon that reassigns the stop codon UAG to pyrrolysine (Pyl), a genetic code variant that results from the biosynthesis of Pyl-tRNA(Pyl). To understand the selective advantage of genetically encoding more than 20 amino acids, we constructed a markerless tRNA(Pyl) deletion strain of Methanosarcina acetivorans (ΔpylT) that cannot decode UAG as Pyl or grow on trimethylamine. Phenotypic defects in the ΔpylT strain were evident in minimal medium containing methanol. Proteomic analyses of wild type (WT) M. acetivorans and ΔpylT cells identified 841 proteins from >7,000 significant peptides detected by MS/MS. Protein production from UAG-containing mRNAs was verified for 19 proteins. Translation of UAG codons was verified by MS/MS for eight proteins, including identification of a Pyl residue in PylB, which catalyzes the first step of Pyl biosynthesis. Deletion of tRNA(Pyl) globally altered the proteome, leading to >300 differentially abundant proteins. Reduction of the genetic code from 21 to 20 amino acids led to significant down-regulation in translation initiation factors, amino acid metabolism, and methanogenesis from methanol, which was offset by a compensatory (100-fold) up-regulation in dimethyl sulfide metabolic enzymes. The data show how a natural proteome adapts to genetic code reduction and indicate that the selective value of an expanded genetic code is related to carbon source range and metabolic efficiency.
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114
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Abstract
Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.
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115
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Aerni HR, Shifman MA, Rogulina S, O'Donoghue P, Rinehart J. Revealing the amino acid composition of proteins within an expanded genetic code. Nucleic Acids Res 2014; 43:e8. [PMID: 25378305 PMCID: PMC4333366 DOI: 10.1093/nar/gku1087] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The genetic code can be manipulated to reassign codons for the incorporation of non-standard amino acids (NSAA). Deletion of release factor 1 in Escherichia coli enhances translation of UAG (Stop) codons, yet may also extended protein synthesis at natural UAG terminated messenger RNAs. The fidelity of protein synthesis at reassigned UAG codons and the purity of the NSAA containing proteins produced require careful examination. Proteomics would be an ideal tool for these tasks, but conventional proteomic analyses cannot readily identify the extended proteins and accurately discover multiple amino acid (AA) insertions at a single UAG. To address these challenges, we created a new proteomic workflow that enabled the detection of UAG readthrough in native proteins in E. coli strains in which UAG was reassigned to encode phosphoserine. The method also enabled quantitation of NSAA and natural AA incorporation at UAG in a recombinant reporter protein. As a proof-of-principle, we measured the fidelity and purity of the phosphoserine orthogonal translation system (OTS) and used this information to improve its performance. Our results show a surprising diversity of natural AAs at reassigned stop codons. Our method can be used to improve OTSs and to quantify amino acid purity at reassigned codons in organisms with expanded genetic codes.
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Affiliation(s)
- Hans R Aerni
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Mark A Shifman
- Keck Biotechnology Resource Laboratory, Yale University, New Haven, CT 06511, USA
| | - Svetlana Rogulina
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Patrick O'Donoghue
- Departments of Biochemistry and Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
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116
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Bröcker MJ, Ho JML, Church GM, Söll D, O'Donoghue P. Recoding the genetic code with selenocysteine. Angew Chem Int Ed Engl 2014; 53:319-23. [PMID: 24511637 DOI: 10.1002/anie.201308584] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Selenocysteine (Sec) is naturally incorporated into proteins by recoding the stop codon UGA. Sec is not hardwired to UGA, as the Sec insertion machinery was found to be able to site-specifically incorporate Sec directed by 58 of the 64 codons. For 15 sense codons, complete conversion of the codon meaning from canonical amino acid (AA) to Sec was observed along with a tenfold increase in selenoprotein yield compared to Sec insertion at the three stop codons. This high-fidelity sense-codon recoding mechanism was demonstrated for Escherichia coli formate dehydrogenase and recombinant human thioredoxin reductase and confirmed by independent biochemical and biophysical methods. Although Sec insertion at UGA is known to compete against protein termination, it is surprising that the Sec machinery has the ability to outcompete abundant aminoacyl-tRNAs in decoding sense codons. The findings have implications for the process of translation and the information storage capacity of the biological cell.
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Haruna KI, Alkazemi MH, Liu Y, Söll D, Englert M. Engineering the elongation factor Tu for efficient selenoprotein synthesis. Nucleic Acids Res 2014; 42:9976-83. [PMID: 25064855 PMCID: PMC4150793 DOI: 10.1093/nar/gku691] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Selenocysteine (Sec) is naturally co-translationally incorporated into proteins by recoding the UGA opal codon with a specialized elongation factor (SelB in bacteria) and an RNA structural signal (SECIS element). We have recently developed a SECIS-free selenoprotein synthesis system that site-specifically—using the UAG amber codon—inserts Sec depending on the elongation factor Tu (EF-Tu). Here, we describe the engineering of EF-Tu for improved selenoprotein synthesis. A Sec-specific selection system was established by expression of human protein O6-alkylguanine-DNA alkyltransferase (hAGT), in which the active site cysteine codon has been replaced by the UAG amber codon. The formed hAGT selenoprotein repairs the DNA damage caused by the methylating agent N-methyl-N′-nitro-N-nitrosoguanidine, and thereby enables Escherichia coli to grow in the presence of this mutagen. An EF-Tu library was created in which codons specifying the amino acid binding pocket were randomized. Selection was carried out for enhanced Sec incorporation into hAGT; the resulting EF-Tu variants contained highly conserved amino acid changes within members of the library. The improved UTu-system with EF-Sel1 raises the efficiency of UAG-specific Sec incorporation to >90%, and also doubles the yield of selenoprotein production.
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Affiliation(s)
- Ken-ichi Haruna
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Muhammad H Alkazemi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Yuchen Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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Hong SH, Kwon YC, Jewett MC. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front Chem 2014; 2:34. [PMID: 24959531 PMCID: PMC4050362 DOI: 10.3389/fchem.2014.00034] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 05/19/2014] [Indexed: 12/20/2022] Open
Abstract
Incorporating non-standard amino acids (NSAAs) into proteins enables new chemical properties, new structures, and new functions. In recent years, improvements in cell-free protein synthesis (CFPS) systems have opened the way to accurate and efficient incorporation of NSAAs into proteins. The driving force behind this development has been three-fold. First, a technical renaissance has enabled high-yielding (>1 g/L) and long-lasting (>10 h in batch operation) CFPS in systems derived from Escherichia coli. Second, the efficiency of orthogonal translation systems (OTSs) has improved. Third, the open nature of the CFPS platform has brought about an unprecedented level of control and freedom of design. Here, we review recent developments in CFPS platforms designed to precisely incorporate NSAAs. In the coming years, we anticipate that CFPS systems will impact efforts to elucidate structure/function relationships of proteins and to make biomaterials and sequence-defined biopolymers for medical and industrial applications.
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Affiliation(s)
- Seok Hoon Hong
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA
| | - Yong-Chan Kwon
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA
| | - Michael C Jewett
- Chemical and Biological Engineering, Northwestern University Evanston, IL, USA ; Chemistry of Life Processes Institute, Northwestern University Evanston, IL, USA ; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL, USA ; Institute of Bionanotechnology in Medicine, Northwestern University Chicago, IL, USA
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119
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Fan C, Ho JML, Chirathivat N, Söll D, Wang YS. Exploring the substrate range of wild-type aminoacyl-tRNA synthetases. Chembiochem 2014; 15:1805-1809. [PMID: 24890918 DOI: 10.1002/cbic.201402083] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Indexed: 01/02/2023]
Abstract
We tested the substrate range of four wild-type E. coli aminoacyl-tRNA synthetases (AARSs) with a library of nonstandard amino acids (nsAAs). Although these AARSs could discriminate efficiently against the other canonical amino acids, they were able to use many nsAAs as substrates. Our results also show that E. coli tryptophanyl-tRNA synthetase (TrpRS) and tyrosyl-tRNA synthetase have overlapping substrate ranges. In addition, we found that the nature of the anticodon sequence of tRNA(Trp) altered the nsAA substrate range of TrpRS; this implies that the sequence of the anticodon affects the TrpRS amino acid binding pocket. These results highlight again that inherent AARS polyspecificity will be a major challenge in the aim of incorporating multiple different amino acids site-specifically into proteins.
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Affiliation(s)
- Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Joanne M L Ho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
| | - Napon Chirathivat
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (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)
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 (USA)
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121
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Bohlke N, Budisa N. Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. FEMS Microbiol Lett 2014; 351:133-44. [PMID: 24433543 PMCID: PMC4237120 DOI: 10.1111/1574-6968.12371] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering.
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Affiliation(s)
- Nina Bohlke
- Department of Chemistry, TU Berlin, Berlin, Germany
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122
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Stafforst T. The selenocysteine incorporation machinery allows the dual use of sense codons: a new strategy for expanding the genetic code? Chembiochem 2013; 15:356-8. [PMID: 24376077 DOI: 10.1002/cbic.201300735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 11/11/2022]
Abstract
Sense and Secis: Even though selenocysteine, Sec, is naturally incorporated by suppressing UAG stop codons, it was recently shown that sense codons such as UAC can efficiently code for Sec. This article highlights the implications of using such a strategy to introduce unnatural amino acids site-selectively into proteins.
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Affiliation(s)
- Thorsten Stafforst
- Interfaculty Institute of Biochemistry, Universität Tübingen, Auf der Morgenstelle 15, 72076 Tübingen (Germany) http://www.ifib.uni-tuebingen.de/research/stafforst.html.
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Krishnakumar R, Ling J. Experimental challenges of sense codon reassignment: an innovative approach to genetic code expansion. FEBS Lett 2013; 588:383-8. [PMID: 24333334 DOI: 10.1016/j.febslet.2013.11.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/19/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
The addition of new and versatile chemical and biological properties to proteins pursued through incorporation of non-canonical amino acids is at present primarily achieved by stop codon suppression. However, it is critical to find new "blank" codons to increase the variety and efficiency of such insertions, thereby taking 'sense codon recoding' to center stage in the field of genetic code expansion. Current thought optimistically suggests the use of the pyrrolysine system coupled with re-synthesis of genomic information towards achieving sense codon reassignment. Upon review of the serious experimental challenges reported in recent studies, we propose that success in this area will depend on the re-synthesis of genomes, but also on 'rewiring' the mechanism of protein synthesis and of its quality control.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Bröcker MJ, Ho JML, Church GM, Söll D, O'Donoghue P. Umkodierung des genetischen Codes mit Selenocystein. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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