1
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Enninful GN, Kuppusamy R, Tiburu EK, Kumar N, Willcox MDP. Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges. J Pept Sci 2024; 30:e3560. [PMID: 38262069 DOI: 10.1002/psc.3560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/01/2023] [Accepted: 11/14/2023] [Indexed: 01/25/2024]
Abstract
The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.
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Affiliation(s)
| | - Rajesh Kuppusamy
- University of New South Wales, Kensington, New South Wales, Australia
| | | | - Naresh Kumar
- University of New South Wales, Kensington, New South Wales, Australia
| | - Mark D P Willcox
- University of New South Wales, Kensington, New South Wales, Australia
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2
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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3
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Seo D, Koh B, Eom GE, Kim HW, Kim S. A dual gene-specific mutator system installs all transition mutations at similar frequencies in vivo. Nucleic Acids Res 2023; 51:e59. [PMID: 37070179 PMCID: PMC10250238 DOI: 10.1093/nar/gkad266] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Targeted in vivo hypermutation accelerates directed evolution of proteins through concurrent DNA diversification and selection. Although systems employing a fusion protein of a nucleobase deaminase and T7 RNA polymerase present gene-specific targeting, their mutational spectra have been limited to exclusive or dominant C:G→T:A mutations. Here we describe eMutaT7transition, a new gene-specific hypermutation system, that installs all transition mutations (C:G→T:A and A:T→G:C) at comparable frequencies. By using two mutator proteins in which two efficient deaminases, PmCDA1 and TadA-8e, are separately fused to T7 RNA polymerase, we obtained similar numbers of C:G→T:A and A:T→G:C substitutions at a sufficiently high frequency (∼6.7 substitutions in 1.3 kb gene during 80-h in vivo mutagenesis). Through eMutaT7transition-mediated TEM-1 evolution for antibiotic resistance, we generated many mutations found in clinical isolates. Overall, with a high mutation frequency and wider mutational spectrum, eMutaT7transition is a potential first-line method for gene-specific in vivo hypermutation.
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Affiliation(s)
- Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Bonghyun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ga-eul Eom
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hye Won Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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4
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Halogenation of tyrosine perturbs large-scale protein self-organization. Nat Commun 2022; 13:4843. [PMID: 35977922 PMCID: PMC9385671 DOI: 10.1038/s41467-022-32535-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022] Open
Abstract
Protein halogenation is a common non-enzymatic post-translational modification contributing to aging, oxidative stress-related diseases and cancer. Here, we report a genetically encodable halogenation of tyrosine residues in a reconstituted prokaryotic filamentous cell-division protein (FtsZ) as a platform to elucidate the implications of halogenation that can be extrapolated to living systems of much higher complexity. We show how single halogenations can fine-tune protein structures and dynamics of FtsZ with subtle perturbations collectively amplified by the process of FtsZ self-organization. Based on experiments and theories, we have gained valuable insights into the mechanism of halogen influence. The bending of FtsZ structures occurs by affecting surface charges and internal domain distances and is reflected in the decline of GTPase activities by reducing GTP binding energy during polymerization. Our results point to a better understanding of the physiological and pathological effects of protein halogenation and may contribute to the development of potential diagnostic tools.
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5
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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6
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Tang H, Zhang P, Luo X. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications. J Mol Biol 2021; 434:167382. [PMID: 34863778 DOI: 10.1016/j.jmb.2021.167382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pan Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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7
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Stieglitz JT, Potts KA, Van Deventer JA. Broadening the Toolkit for Quantitatively Evaluating Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2021; 10:3094-3104. [PMID: 34730946 DOI: 10.1021/acssynbio.1c00370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion is a powerful approach for advancing critical fields such as biological therapeutic discovery. However, the machinery for genetically encoding noncanonical amino acids (ncAAs) is only available in limited plasmid formats, constraining potential applications. In extreme cases, the introduction of two separate plasmids, one containing an orthogonal translation system (OTS) to facilitate ncAA incorporation and a second for expressing a ncAA-containing protein of interest, is not possible due to a lack of the available selection markers. One strategy to circumvent this challenge is to express the OTS and protein of interest from a single vector. For what we believe is the first time in yeast, we describe here several sets of single plasmid systems (SPSs) for performing genetic code manipulation and compare the ncAA incorporation capabilities of these plasmids against the capabilities of previously described dual plasmid systems (DPSs). For both dual fluorescent protein reporters and yeast display reporters tested with multiple OTSs and ncAAs, measured ncAA incorporation efficiencies with SPSs were determined to be equal to efficiencies determined with DPSs. Click chemistry on yeast cells displaying ncAA-containing proteins was also shown to be feasible in both formats, although differences in reactivity between formats suggest the need for caution when using such approaches. Additionally, we investigated whether these reporters would support the separation of yeast strains known to exhibit distinct ncAA incorporation efficiencies. Model sorts conducted with mixtures of two strains transformed with the same SPS or DPS both led to the enrichment of a strain known to support a higher efficiency ncAA incorporation, suggesting that these reporters will be suitable for conducting screens for strains exhibiting enhanced ncAA incorporation efficiencies. Overall, our results confirm that SPSs are well behaved in yeast and provide a convenient alternative to DPSs. SPSs are expected to be invaluable for conducting high-throughput investigations of the effects of genetic or genomic changes on ncAA incorporation efficiency and, more fundamentally, the eukaryotic translation apparatus.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Kelly A. Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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8
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Dual genetic selection of the theophylline riboswitch with altered aptamer specificity for caffeine. Biochem Biophys Res Commun 2021; 579:105-109. [PMID: 34597992 DOI: 10.1016/j.bbrc.2021.09.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/21/2022]
Abstract
The aptamer domain of the theophylline riboswitch was randomized to generate a library containing millions of different variants. Dual genetic selection utilizing the cat-upp fusion gene was performed for the library, which successfully led to the identification of a caffeine-specific synthetic riboswitch. When a chloramphenicol-resistance gene was expressed under control of this riboswitch, E. coli cells showed chloramphenicol resistance only in the presence of caffeine. When inserted upstream of the gfpuv or lacZ gene, the caffeine riboswitch induced the expression of green fluorescent protein or β-galactosidase in the presence of caffeine, respectively. When tested with various concentrations of caffeine, the β-galactosidase activity was proportional to the amount of caffeine, clearly indicating the caffeine-dependent gene regulation by the caffeine riboswitch.
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9
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Park H, Kim S. Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo. Nucleic Acids Res 2021; 49:e32. [PMID: 33406230 PMCID: PMC8034631 DOI: 10.1093/nar/gkaa1231] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 01/21/2023] Open
Abstract
Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in vivo mutation rate and high gene-specificity in Escherichia coli. eMutaT7, a cytidine deaminase fused to an orthogonal RNA polymerase, can introduce up to ∼4 mutations per 1 kb per day, rivalling the rate in typical in vitro mutagenesis for directed evolution of proteins, and promotes rapid continuous evolution of model proteins for antibiotic resistance and allosteric activation. eMutaT7 provides a very simple and tunable method for continuous directed evolution of proteins, and suggests that the fusion of new DNA-modifying enzymes to the orthogonal RNA polymerase is a promising strategy to explore the expanded sequence space without compromising gene specificity.
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Affiliation(s)
- Hyojin Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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10
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Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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11
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An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli. Bioorg Med Chem 2020; 28:115662. [PMID: 33069069 DOI: 10.1016/j.bmc.2020.115662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/18/2020] [Indexed: 11/24/2022]
Abstract
We report the development of the orthogonal amber-suppressor pair Archaeoglobus fulgidus seryl-tRNA (Af-tRNASer)/Methanosarcina mazei seryl-tRNA synthetase (MmSerRS) in Escherichia coli. Furthermore, the crystal structure of MmSerRS was solved at 1.45 Å resolution, which should enable structure-guided engineering of its active site to genetically encode small, polar noncanonical amino acids (ncAAs).
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12
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Engineered ribosomes with tethered subunits for expanding biological function. Nat Commun 2019; 10:3920. [PMID: 31477696 PMCID: PMC6718428 DOI: 10.1038/s41467-019-11427-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/10/2019] [Indexed: 01/01/2023] Open
Abstract
Ribo-T is a ribosome with covalently tethered subunits where core 16S and 23S ribosomal RNAs form a single chimeric molecule. Ribo-T makes possible a functionally orthogonal ribosome-mRNA system in cells. Unfortunately, use of Ribo-T has been limited because of low activity of its original version. Here, to overcome this limitation, we use an evolutionary approach to select new tether designs that are capable of supporting faster cell growth and increased protein expression. Further, we evolve new orthogonal Ribo-T/mRNA pairs that function in parallel with, but independent of, natural ribosomes and mRNAs, increasing the efficiency of orthogonal protein expression. The Ribo-T with optimized designs is able to synthesize a diverse set of proteins, and can also incorporate multiple non-canonical amino acids into synthesized polypeptides. The enhanced Ribo-T designs should be useful for exploring poorly understood functions of the ribosome and engineering ribosomes with altered catalytic properties.
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13
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Chan SN, Low END, Raja Ali RA, Mokhtar NM. Delineating inflammatory bowel disease through transcriptomic studies: current review of progress and evidence. Intest Res 2018; 16:374-383. [PMID: 30090036 PMCID: PMC6077315 DOI: 10.5217/ir.2018.16.3.374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), which comprises of Crohn's disease and ulcerative colitis, is an idiopathic relapsing and remitting disease in which the interplay of different environment, microbial, immunological and genetic factors that attribute to the progression of the disease. Numerous studies have been conducted in multiple aspects including clinical, endoscopy and histopathology for the diagnostics and treatment of IBD. However, the molecular mechanism underlying the aetiology and pathogenesis of IBD is still poorly understood. This review tries to critically assess the scientific evidence at the transcriptomic level as it would help in the discovery of RNA molecules in tissues or serum between the healthy and diseased or different IBD subtypes. These molecular signatures could potentially serve as a reliable diagnostic or prognostic biomarker. Researchers have also embarked on the study of transcriptome to be utilized in targeted therapy. We focus on the evaluation and discussion related to the publications reporting the different approaches and techniques used in investigating the transcriptomic changes in IBD with the intention to offer new perspectives to the landscape of the disease.
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Affiliation(s)
- Seow-Neng Chan
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Eden Ngah Den Low
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
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14
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Fladischer P, Weingartner A, Blamauer J, Darnhofer B, Birner-Gruenberger R, Kardashliev T, Ruff AJ, Schwaneberg U, Wiltschi B. A Semi-Rationally Engineered Bacterial Pyrrolysyl-tRNA Synthetase Genetically Encodes Phenyl Azide Chemistry. Biotechnol J 2018; 14:e1800125. [DOI: 10.1002/biot.201800125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/25/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Patrik Fladischer
- Acib − Austrian Centre of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Graz Austria
| | - Alexandra Weingartner
- Acib − Austrian Centre of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Graz Austria
| | - Johannes Blamauer
- Acib − Austrian Centre of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Graz Austria
| | - Barbara Darnhofer
- Acib − Austrian Centre of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
- Research Unit Functional Proteomics and Metabolomic Pathways; Institute of Pathology; Medical University of Graz; Graz Austria
- Omics Center Graz; BioTechMed-Graz; Graz Austria
| | - Ruth Birner-Gruenberger
- Research Unit Functional Proteomics and Metabolomic Pathways; Institute of Pathology; Medical University of Graz; Graz Austria
- Omics Center Graz; BioTechMed-Graz; Graz Austria
| | | | - Anna Joelle Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Aachen Germany
| | | | - Birgit Wiltschi
- Acib − Austrian Centre of Industrial Biotechnology; Petersgasse 14 A-8010 Graz Austria
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15
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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16
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Ferreira Amaral MM, Frigotto L, Hine AV. Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis-Methodologies and Advantages. Methods Enzymol 2017; 585:111-133. [PMID: 28109425 DOI: 10.1016/bs.mie.2016.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity.
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Affiliation(s)
- M M Ferreira Amaral
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - L Frigotto
- Isogenica Ltd., The Mansion, Chesterford Research Park, Essex, United Kingdom
| | - A V Hine
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom.
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17
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Italia JS, Addy PS, Wrobel CJJ, Crawford LA, Lajoie MJ, Zheng Y, Chatterjee A. An orthogonalized platform for genetic code expansion in both bacteria and eukaryotes. Nat Chem Biol 2017; 13:446-450. [PMID: 28192410 DOI: 10.1038/nchembio.2312] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/12/2016] [Indexed: 11/09/2022]
Abstract
In this study, we demonstrate the feasibility of expanding the genetic code of Escherichia coli using its own tryptophanyl-tRNA synthetase and tRNA (TrpRS-tRNATrp) pair. This was made possible by first functionally replacing this endogenous pair with an E. coli-optimized counterpart from Saccharomyces cerevisiae, and then reintroducing the liberated E. coli TrpRS-tRNATrp pair into the resulting strain as a nonsense suppressor, which was then followed by its directed evolution to genetically encode several new unnatural amino acids (UAAs). These engineered TrpRS-tRNATrp variants were also able to drive efficient UAA mutagenesis in mammalian cells. Since bacteria-derived aminoacyl-tRNA synthetase (aaRS)-tRNA pairs are typically orthogonal in eukaryotes, our work provides a general strategy to develop additional aaRS-tRNA pairs that can be used for UAA mutagenesis of proteins expressed in both E. coli and eukaryotes.
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Affiliation(s)
- James S Italia
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | | | - Chester J J Wrobel
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - Lisa A Crawford
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Yunan Zheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
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18
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Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol Bioeng 2017; 114:1074-1086. [PMID: 27987323 DOI: 10.1002/bit.26239] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/28/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023]
Abstract
The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-0001.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Simpson Querry Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
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19
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Leisle L, Valiyaveetil F, Mehl RA, Ahern CA. Incorporation of Non-Canonical Amino Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 869:119-51. [PMID: 26381943 DOI: 10.1007/978-1-4939-2845-3_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter we discuss the strengths, caveats and technical considerations of three approaches for reprogramming the chemical composition of selected amino acids within a membrane protein. In vivo nonsense suppression in the Xenopus laevis oocyte, evolved orthogonal tRNA and aminoacyl-tRNA synthetase pairs and protein ligation for biochemical production of semisynthetic proteins have been used successfully for ion channel and receptor studies. The level of difficulty for the application of each approach ranges from trivial to technically demanding, yet all have untapped potential in their application to membrane proteins.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA
| | - Francis Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health and Sciences University, 97239, Portland, OR, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University Corvallis, 97331, Corvallis, OR, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, 51 Newton Road, 52246, Iowa City, IA, USA.
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20
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Wals K, Ovaa H. Unnatural amino acid incorporation in E. coli: current and future applications in the design of therapeutic proteins. Front Chem 2014; 2:15. [PMID: 24790983 PMCID: PMC3982533 DOI: 10.3389/fchem.2014.00015] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/10/2014] [Indexed: 01/26/2023] Open
Abstract
Unnatural amino acid (UAA) incorporation by amber codon suppression offers scientists a powerful tool to modify the properties of proteins at will. UAA incorporation has been used for a plethora of fundamental research applications and, more recently, also for the selective modification of therapeutic proteins. In this review most recent developments in Escherichia coli codon expansion and, unnatural amino acid incorporation are discussed together with some remarkable recent developments in improved efficient UAA incorporation. We focus on the generation of proteins that hold promise for future therapeutic applications that would be impossible to obtain without unnatural amino acid incorporation, including the generation of bi-specific antibodies and antibody drug conjugates.
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Affiliation(s)
| | - Huib Ovaa
- Division of Cell Biology, Chemical Biology and Drug Innovation, The Netherlands Cancer InstituteAmsterdam, Netherlands
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21
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Kaltenbach M, Tokuriki N. Dynamics and constraints of enzyme evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:468-87. [DOI: 10.1002/jez.b.22562] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories; University of British Columbia; Vancouver British Columbia Canada
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22
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Zimmerman ES, Heibeck TH, Gill A, Li X, Murray CJ, Madlansacay MR, Tran C, Uter NT, Yin G, Rivers PJ, Yam AY, Wang WD, Steiner AR, Bajad SU, Penta K, Yang W, Hallam TJ, Thanos CD, Sato AK. Production of site-specific antibody-drug conjugates using optimized non-natural amino acids in a cell-free expression system. Bioconjug Chem 2014; 25:351-61. [PMID: 24437342 DOI: 10.1021/bc400490z] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Antibody-drug conjugates (ADCs) are a targeted chemotherapeutic currently at the cutting edge of oncology medicine. These hybrid molecules consist of a tumor antigen-specific antibody coupled to a chemotherapeutic small molecule. Through targeted delivery of potent cytotoxins, ADCs exhibit improved therapeutic index and enhanced efficacy relative to traditional chemotherapies and monoclonal antibody therapies. The currently FDA-approved ADCs, Kadcyla (Immunogen/Roche) and Adcetris (Seattle Genetics), are produced by conjugation to surface-exposed lysines, or partial disulfide reduction and conjugation to free cysteines, respectively. These stochastic modes of conjugation lead to heterogeneous drug products with varied numbers of drugs conjugated across several possible sites. As a consequence, the field has limited understanding of the relationships between the site and extent of drug loading and ADC attributes such as efficacy, safety, pharmacokinetics, and immunogenicity. A robust platform for rapid production of ADCs with defined and uniform sites of drug conjugation would enable such studies. We have established a cell-free protein expression system for production of antibody drug conjugates through site-specific incorporation of the optimized non-natural amino acid, para-azidomethyl-l-phenylalanine (pAMF). By using our cell-free protein synthesis platform to directly screen a library of aaRS variants, we have discovered a novel variant of the Methanococcus jannaschii tyrosyl tRNA synthetase (TyrRS), with a high activity and specificity toward pAMF. We demonstrate that site-specific incorporation of pAMF facilitates near complete conjugation of a DBCO-PEG-monomethyl auristatin (DBCO-PEG-MMAF) drug to the tumor-specific, Her2-binding IgG Trastuzumab using strain-promoted azide-alkyne cycloaddition (SPAAC) copper-free click chemistry. The resultant ADCs proved highly potent in in vitro cell cytotoxicity assays.
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Affiliation(s)
- Erik S Zimmerman
- Sutro Biopharma, Inc. 310 Utah Ave Suite 150 South San Francisco, California 94080, United States
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23
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Chen S, Tsao ML. Genetic Incorporation of a 2-Naphthol Group into Proteins for Site-Specific Azo Coupling. Bioconjug Chem 2013; 24:1645-9. [DOI: 10.1021/bc400168u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shuo Chen
- Chemistry and Chemical Biology
Group, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
| | - Meng-Lin Tsao
- Chemistry and Chemical Biology
Group, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
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24
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Making connections--strategies for single molecule fluorescence biophysics. Curr Opin Chem Biol 2013; 17:691-8. [PMID: 23769868 PMCID: PMC3989056 DOI: 10.1016/j.cbpa.2013.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/02/2013] [Accepted: 05/17/2013] [Indexed: 11/28/2022]
Abstract
The single-molecule approach yields exciting insights for many biomolecular applications. There are significant challenges to achieve main-stream single-molecule measurements. New labelling chemistries enable multiple tagged molecules in vitro and in live cells. Single-molecule pull-down expands the toolbox complementing co-immunoprecipitation. Breaking the single-molecule concentration barrier is within reach.
Fluorescence spectroscopy and fluorescence microscopy carried out on the single molecule level are elegant methods to decipher complex biological systems; it can provide a wealth of information that frequently is obscured in the averaging of ensemble measurements. Fluorescence can be used to localise a molecule, study its binding with interaction partners and ligands, or to follow conformational changes in large multicomponent systems. Efficient labelling of proteins and nucleic acids is very important for any fluorescence method, and equally the development of novel fluorophores has been crucial in making biomolecules amenable to single molecule fluorescence methods. In this paper we review novel coupling strategies that permit site-specific and efficient labelling of proteins. Furthermore, we will discuss progressive single molecule approaches that allow the detection of individual molecules and biomolecular complexes even directly isolated from cellular extracts at much higher and much lower concentrations than has been possible so far.
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25
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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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26
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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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27
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Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 2012; 109:14841-6. [PMID: 22927411 DOI: 10.1073/pnas.1212454109] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The site-specific incorporation of unnatural amino acids (UAAs) into proteins in living cells relies on an engineered tRNA/aminoacyl-tRNA synthetase (tRNA/aaRS) pair, orthogonal to the host cell, to deliver the UAA of choice in response to a unique nonsense or frameshift codon. Here we report the generation of mutually orthogonal prolyl-tRNA/prolyl-tRNA synthase (ProRS) pairs derived from an archaebacterial ancestor for use in Escherichia coli. By reprogramming the anticodon-binding pocket of Pyrococcus horikoshii ProRS (PhProRS), we were able to identify synthetase variants that recognize engineered Archaeoglobus fulgidus prolyl-tRNAs (Af-tRNA(Pro)) with three different anticodons: CUA, AGGG, and CUAG. Several of these evolved PhProRSs show specificity toward a particular anticodon variant of Af-tRNA(Pro), whereas others are promiscuous. Further evolution of the Af-tRNA(Pro) led to a variant exhibiting significantly improved amber suppression efficiency. Availability of a prolyl-tRNA/aaRS pair should enable site-specific incorporation of proline analogs and other N-modified UAAs into proteins in E. coli. The evolution of mutually orthogonal prolyl-tRNA/ProRS pairs demonstrates the plasticity of the tRNA-aaRS interface and should facilitate the incorporation of multiple, distinct UAAs into proteins.
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28
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Cobb RE, Sun N, Zhao H. Directed evolution as a powerful synthetic biology tool. Methods 2012; 60:81-90. [PMID: 22465795 DOI: 10.1016/j.ymeth.2012.03.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 03/09/2012] [Indexed: 01/31/2023] Open
Abstract
At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels.
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Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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29
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Wang YS, Fang X, Wallace AL, Wu B, Liu WR. A rationally designed pyrrolysyl-tRNA synthetase mutant with a broad substrate spectrum. J Am Chem Soc 2012; 134:2950-3. [PMID: 22289053 PMCID: PMC3288562 DOI: 10.1021/ja211972x] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Together with tRNA(CUA)(Pyl), a rationally designed pyrrolysyl-tRNA synthetase mutant N346A/C348A has been successfully used for the genetic incorporation of a variety of phenylalanine derivatives with large para substituents into superfolder green fluorescent protein at an amber mutation site in Escherichia coli. This discovery greatly expands the genetically encoded noncanonical amino acid inventory and opens the gate for the genetic incorporation of other phenylalanine derivatives using engineered pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs.
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Affiliation(s)
- Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xinqiang Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ashley L. Wallace
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bo Wu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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30
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Importance of single molecular determinants in the fidelity of expanded genetic codes. Proc Natl Acad Sci U S A 2011; 108:1320-5. [PMID: 21224416 DOI: 10.1073/pnas.1012276108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The site-selective encoding of noncanonical amino acids (NAAs) is a powerful technique for the installation of novel chemical functional groups in proteins. This is often achieved by recoding a stop codon and requires two additional components: an evolved aminoacyl tRNA synthetase (AARS) and a cognate tRNA. Analysis of the most successful AARSs reveals common characteristics. The highest fidelity NAA systems derived from the Methanocaldococcus jannaschii tyrosyl AARS feature specific mutations to two residues reported to interact with the hydroxyl group of the substrate tyrosine. We demonstrate that the restoration of just one of these determinants for amino acid specificity results in the loss of fidelity as the evolved AARSs become noticeably promiscuous. These results offer a partial explanation of a recently retracted strategy for the synthesis of glycoproteins. Similarly, we reinvestigated a tryptophanyl AARS reported to allow the site-selective incorporation of 5-hydroxy tryptophan within mammalian cells. In multiple experiments, the enzyme displayed elements of promiscuity despite its previous characterization as a high fidelity enzyme. Given the many similarities of the TyrRSs and TrpRSs reevaluated here, our findings can be largely combined, and in doing so they reinforce the long-established central dogma regarding the molecular basis by which these enzymes contribute to the fidelity of translation. Thus, our view is that the central claims of fidelity reported in several NAA systems remain unproven and unprecedented.
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31
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Engineering of an Orthogonal Aminoacyl-tRNA Synthetase for Efficient Incorporation of the Non-natural Amino Acid O-Methyl-L-tyrosine using Fluorescence-based Bacterial Cell Sorting. J Mol Biol 2010; 404:70-87. [DOI: 10.1016/j.jmb.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 08/14/2010] [Accepted: 09/01/2010] [Indexed: 11/18/2022]
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32
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33
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Miyake-Stoner SJ, Refakis CA, Hammill JT, Lusic H, Hazen JL, Deiters A, Mehl RA. Generating permissive site-specific unnatural aminoacyl-tRNA synthetases. Biochemistry 2010; 49:1667-77. [PMID: 20082521 DOI: 10.1021/bi901947r] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genetically incorporated unnatural amino acid (UAA) technologies are powerful tools that are greatly enhancing our ability to study and engineer biological systems. Using these techniques, researchers can precisely control the position and number of novel chemical moieties in a protein, via introducing the novel R group of UAAs, that are genetically encoded in the protein's primary structure. The substrate recognition properties of a natural aminoacyl-tRNA synthetase (aaRS) must be modified in order to incorporate UAAs into proteins. Protocols to do so are technically simple but require time and optimization, which has significantly limited the accessibility of this important technology. At present, engineered unnatural aminoacyl-tRNA synthetases (UaaRS) are evaluated on their translational efficiency (the extent to which they allow for incorporation of UAAs into protein) and fidelity (the extent to which they prevent incorporation of natural amino acids). We propose that a third parameter of substrate recognition, permissivity, is equally important. Permissive UaaRSs, whose relaxed substrate recognition properties allow them to incorporate multiple unnatural amino acids (but not natural amino acids), would eliminate the need to generate new UaaRSs for many new UAAs. Here, we outline methods for quickly and easily assessing the permissivity of existing UaaRSs and for generating permissive UaaRSs. In proof of principle experiments, we determined the degree of permissivity of two UaaRSs for a family of structurally related fluorinated UAAs ((19)F-UAAs). We then increased the permissivity of the initial UaaRSs to allow for incorporation of the family of (19)F-UAAs. Finally, we validated the utility of these new (19)F-UAAs as probes for fluorine NMR studies of protein structure and dynamics. We expect that results of this work will increase the accessibility of UAA technology and the use of new UAAs in proteins.
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Affiliation(s)
- Shigeki J Miyake-Stoner
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
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34
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35
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Voloshchuk N, Montclare JK. Incorporation of unnatural amino acids for synthetic biology. ACTA ACUST UNITED AC 2010; 6:65-80. [DOI: 10.1039/b909200p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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Minnihan EC, Yokoyama K, Stubbe J. Unnatural amino acids: better than the real things? F1000 BIOLOGY REPORTS 2009; 1:88. [PMID: 20948602 PMCID: PMC2948271 DOI: 10.3410/b1-88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Considerable effort has been dedicated to the development of technology for the site-specific incorporation of unnatural amino acids into proteins, with nonsense codon suppression and expressed protein ligation emerging as two of the most promising methods. Recent research advances in which these methods have been applied to study protein function and mechanism are briefly highlighted, and the potential of the methods for efficient, widespread future use in vitro and in vivo is critically evaluated.
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Affiliation(s)
- Ellen C Minnihan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA
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