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Opuu V, Nigro G, Lazennec‐Schurdevin C, Mechulam Y, Schmitt E, Simonson T. Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments. Protein Sci 2023; 32:e4738. [PMID: 37518893 PMCID: PMC10451022 DOI: 10.1002/pro.4738] [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: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023]
Abstract
Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate aminoacyl-tRNA synthetase. Currently, directed evolution is not available to optimize AAs with noncanonical backbones, since an appropriate selective pressure has not been discovered. Computational protein design (CPD) is an alternative. We used a new CPD method to redesign MetRS and increase its activity towards β-Met, which has an extra backbone methylene. The new method considered a few active site positions for design and used a Monte Carlo exploration of the corresponding sequence space. During the exploration, a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to their β-Met binding affinities. Eighteen predicted variants were chosen for experimental testing; 10 exhibited detectable activity for β-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for both α-Met and β-Met were measured. The best mutant retained a preference for α-Met over β-Met; however, the preference was reduced, compared to the wildtype, by a factor of 29. For this mutant, high resolution crystal structures were obtained in complex with both α-Met and β-Met, indicating that the predicted, active conformation of β-Met in the active site was retained.
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Affiliation(s)
- Vaitea Opuu
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Giuliano Nigro
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Christine Lazennec‐Schurdevin
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
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2
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Opuu V, Simonson T. Enzyme redesign and genetic code expansion. Protein Eng Des Sel 2023; 36:gzad017. [PMID: 37879093 DOI: 10.1093/protein/gzad017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Enzyme design is an important application of computational protein design (CPD). It can benefit enormously from the additional chemistries provided by noncanonical amino acids (ncAAs). These can be incorporated into an 'expanded' genetic code, and introduced in vivo into target proteins. The key step for genetic code expansion is to engineer an aminoacyl-transfer RNA (tRNA) synthetase (aaRS) and an associated tRNA that handles the ncAA. Experimental directed evolution has been successfully used to engineer aaRSs and incorporate over 200 ncAAs into expanded codes. But directed evolution has severe limits, and is not yet applicable to noncanonical AA backbones. CPD can help address several of its limitations, and has begun to be applied to this problem. We review efforts to redesign aaRSs, studies that designed new proteins and functionalities with the help of ncAAs, and some of the method developments that have been used, such as adaptive landscape flattening Monte Carlo, which allows an enzyme to be redesigned with substrate or transition state binding as the design target.
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Affiliation(s)
- Vaitea Opuu
- Institut Chimie Biologie Innovation (CNRS UMR8231), Ecole Supérieure de Physique et Chimie de Paris (ESPCI), 75005 Paris, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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3
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Shi N, Tong L, Lin H, Zheng Z, Zhang H, Dong L, Yang Y, Shen Y, Xia Q. Optimizing eRF1 to Enable the Genetic Encoding of Three Distinct Noncanonical Amino Acids in Mammalian Cells. Adv Biol (Weinh) 2022; 6:e2200092. [PMID: 35818694 DOI: 10.1002/adbi.202200092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Indexed: 01/28/2023]
Abstract
Site-specific incorporation of distinct noncanonical amino acids (ncAAs) into proteins via genetic code expansion in mammalian cells represents a new avenue for protein engineering. Reassigning three TAGs with the same ncAA in mammalian cells has previously been achieved using translational machinery. However, simultaneous recoding of three nonsense codons with distinct ncAAs in mammalian cells remains a challenge due to low incorporation efficiencies. Here, three optimized aaRS/tRNA pairs (i.e., the E. coli-derived tyrosyl (EcTyr)/tRNAUUA , E. coli-derived leucyl (EcLeu)/tRNACUA , and Methanosarcina mazei pyrrolysyl (MmPyl)/tRNAUCA pairs) are screened for ncAA incorporation. Furthermore, introduced combinations of eukaryotic release factor 1 (eRF1) mutants (E55R, E55D, N129D, and Y125F) significantly improve the encoding efficiency of the three premature stop codons' sites from 0.78% to 11.6%. Thus, site-specific incorporation of three distinct ncAAs into a single protein is achieved in this study. This work markedly expands the potential for multiple site-specific protein modifications within mammalian cells, thereby facilitating new in vivo applications.
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Affiliation(s)
- Ningning Shi
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Le Tong
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Haishuang Lin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhetao Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Haoran Zhang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Liangzhen Dong
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yuelin Yang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yuxuan Shen
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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4
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Krebs SK, Rakotoarinoro N, Stech M, Zemella A, Kubick S. A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality. Front Bioeng Biotechnol 2022; 10:873906. [PMID: 35573244 PMCID: PMC9098822 DOI: 10.3389/fbioe.2022.873906] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein’s coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyrCUA were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
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Affiliation(s)
- Simon K. Krebs
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin, Berlin, Germany
| | - Nathanaël Rakotoarinoro
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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5
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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6
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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7
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Pérez-Mejías G, Velázquez-Cruz A, Guerra-Castellano A, Baños-Jaime B, Díaz-Quintana A, González-Arzola K, Ángel De la Rosa M, Díaz-Moreno I. Exploring protein phosphorylation by combining computational approaches and biochemical methods. Comput Struct Biotechnol J 2020; 18:1852-1863. [PMID: 32728408 PMCID: PMC7369424 DOI: 10.1016/j.csbj.2020.06.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications of proteins expand their functional diversity, regulating the response of cells to a variety of stimuli. Among these modifications, phosphorylation is the most ubiquitous and plays a prominent role in cell signaling. The addition of a phosphate often affects the function of a protein by altering its structure and dynamics. However, these alterations are often difficult to study and the functional and structural implications remain unresolved. New approaches are emerging to overcome common obstacles related to the production and manipulation of these samples. Here, we summarize the available methods for phosphoprotein purification and phosphomimetic engineering, highlighting the advantages and disadvantages of each. We propose a general workflow for protein phosphorylation analysis combining computational and biochemical approaches, building on recent advances that enable user-friendly and easy-to-access Molecular Dynamics simulations. We hope this innovative workflow will inform the best experimental approach to explore such post-translational modifications. We have applied this workflow to two different human protein models: the hemeprotein cytochrome c and the RNA binding protein HuR. Our results illustrate the usefulness of Molecular Dynamics as a decision-making tool to design the most appropriate phosphomimetic variant.
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Affiliation(s)
- Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Katiuska González-Arzola
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Miguel Ángel De la Rosa
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda., Américo Vespucio 49, Sevilla 41092, Spain
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8
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Wesalo JS, Luo J, Morihiro K, Liu J, Deiters A. Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation. Chembiochem 2020; 21:141-148. [PMID: 31664790 PMCID: PMC6980333 DOI: 10.1002/cbic.201900464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/03/2019] [Indexed: 11/06/2022]
Abstract
The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small-molecule triggers that turn on proteins through a Staudinger reduction/self-immolation cascade with substantially improved kinetics and yields. We achieved this through site-specific incorporation of a new set of azidobenzyloxycarbonyl lysine derivatives in mammalian cells. This approach allowed us to activate proteins by adding a nontoxic, bioorthogonal phosphine trigger. We applied this methodology to control a post-translational modification (SUMOylation) in live cells, using native modification machinery. This work significantly improves the rate, yield, and tunability of the Staudinger reduction-based activation, paving the way for its application in other proteins and organisms.
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Affiliation(s)
- Joshua S. Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Kunihiko Morihiro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
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9
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Des Soye BJ, Gerbasi VR, Thomas PM, Kelleher NL, Jewett MC. A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli. Cell Chem Biol 2019; 26:1743-1754.e9. [PMID: 31706984 DOI: 10.1016/j.chembiol.2019.10.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 (RF1) competition has limited this technology. To address this limitation, we develop a high-yield, one-pot cell-free platform for synthesizing proteins bearing ncAAs based on genomically recoded Escherichia coli lacking RF1. A key feature of this platform is the independence on the addition of purified T7 DNA-directed RNA polymerase (T7RNAP) to catalyze transcription. Extracts derived from our final strain demonstrate high productivity, synthesizing 2.67 ± 0.06 g/L superfolder GFP in batch mode without supplementation of purified T7RNAP. Using an optimized one-pot platform, we demonstrate multi-site incorporation of the ncAA p-acetyl-L-phenylalanine into an elastin-like polypeptide with high accuracy of incorporation and yield. Our work has implications for chemical and synthetic biology.
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Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Vincent R Gerbasi
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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10
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Budisa N, Schneider T. Expanding the DOPA Universe with Genetically Encoded, Mussel-Inspired Bioadhesives for Material Sciences and Medicine. Chembiochem 2019; 20:2163-2190. [PMID: 30830997 DOI: 10.1002/cbic.201900030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
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Affiliation(s)
- Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany.,Chair of Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2, Winnipeg, MB, Canada
| | - Tobias Schneider
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
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11
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Baumann T, Hauf M, Richter F, Albers S, Möglich A, Ignatova Z, Budisa N. Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine. Int J Mol Sci 2019; 20:ijms20092343. [PMID: 31083552 PMCID: PMC6539999 DOI: 10.3390/ijms20092343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/20/2023] Open
Abstract
Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants. For aaRS enzyme redesign, photocaged ortho-nitrobenzyl tyrosine (ONBY) was chosen as substrate due to commercial availability and its diverse applications. Diversifying 17 first- and second-shell sites and performing conventional aaRS positive and negative selection resulted in a high-activity aaRS. This MjTyrRS variant carries ten mutations and outperforms previously reported ONBY-specific aaRS variants isolated from traditional libraries. In response to a single in-frame amber stop codon, it mediates the in vivo incorporation of ONBY with an efficiency matching that of the wild type MjTyrRS enzyme acylating cognate tyrosine. These results exemplify an improved general strategy for aaRS library design and engineering.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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12
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Kato Y. Translational Control using an Expanded Genetic Code. Int J Mol Sci 2019; 20:ijms20040887. [PMID: 30781713 PMCID: PMC6412442 DOI: 10.3390/ijms20040887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan.
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13
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Tippmann EM, Culpepper S, Bunnel W, Appel N. New perspectives on aryl azide noncanonical amino acid use in yeast. Photochem Photobiol Sci 2019; 18:253-258. [DOI: 10.1039/c8pp00243f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A photochemically chemically active noncanonical amino acidpara-azido-l-phenylalanine widely used in biology was found to be metabolized bySaccharomyces cerevisiae.
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14
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Sungwienwong I, Hostetler ZM, Blizzard RJ, Porter JJ, Driggers CM, Mbengi LZ, Villegas JA, Speight LC, Saven JG, Perona JJ, Kohli RM, Mehl RA, Petersson EJ. Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection. Org Biomol Chem 2018; 15:3603-3610. [PMID: 28397914 DOI: 10.1039/c7ob00582b] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein dynamics, either alone or as part of a Förster resonance energy transfer (FRET) or photo-induced electron transfer (eT) probe pair. We have previously reported the genetic incorporation of Acd by an aminoacyl tRNA synthetase (RS). However, this RS, developed from a library of permissive RSs, also incorporates N-phenyl-aminophenylalanine (Npf), a trace byproduct of one Acd synthetic route. We have performed negative selections in the presence of Npf and analyzed the selectivity of the resulting AcdRSs by in vivo protein expression and detailed kinetic analyses of the purified RSs. We find that selection conferred a ∼50-fold increase in selectivity for Acd over Npf, eliminating incorporation of Npf contaminants, and allowing one to use a high yielding Acd synthetic route for improved overall expression of Acd-containing proteins. More generally, our report also provides a cautionary tale on the use of permissive RSs, as well as a strategy for improving selectivity for the target amino acid.
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Affiliation(s)
- Itthipol Sungwienwong
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
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15
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From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies. Angew Chem Int Ed Engl 2018; 57:4313-4328. [DOI: 10.1002/anie.201707976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/14/2017] [Indexed: 12/20/2022]
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16
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Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM. Vom Design der Moleküle des Lebens zum Design von Leben: Zukünftige Anwendungen von DNA-Technologien. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201707976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Richie E. Kohman
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | | | - Eriona Hysolli
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
| | - Yu Wang
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | - George M. Church
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
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17
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Abstract
Accurate incorporation of nonstandard amino acids (nsAAs) is central for genetic code expansion to increase the chemical diversity of proteins. However, aminoacyl-tRNA synthetases are polyspecific and facilitate incorporation of multiple nsAAs. We investigated and repurposed a natural protein degradation pathway, the N-end rule pathway, to devise an innovative system for rapid assessment of the accuracy of nsAA incorporation. Using this tool to monitor incorporation of the nsAA biphenylalanine allowed the identification of tyrosyl-tRNA synthetase (TyrRS) variants with improved amino acid specificity. The evolved TyrRS variants enhanced our ability to contain unwanted proliferation of genetically modified organisms. This posttranslational proofreading system will aid the evolution of orthogonal translation systems for specific incorporation of diverse nsAAs. Incorporation of nonstandard amino acids (nsAAs) leads to chemical diversification of proteins, which is an important tool for the investigation and engineering of biological processes. However, the aminoacyl-tRNA synthetases crucial for this process are polyspecific in regard to nsAAs and standard amino acids. Here, we develop a quality control system called “posttranslational proofreading” to more accurately and rapidly evaluate nsAA incorporation. We achieve this proofreading by hijacking a natural pathway of protein degradation known as the N-end rule, which regulates the lifespan of a protein based on its amino-terminal residue. We find that proteins containing certain desired N-terminal nsAAs have much longer half-lives compared with those proteins containing undesired amino acids. We use the posttranslational proofreading system to further evolve a Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (TyrRS) variant and a tRNATyr species for improved specificity of the nsAA biphenylalanine in vitro and in vivo. Our newly evolved biphenylalanine incorporation machinery enhances the biocontainment and growth of genetically engineered Escherichia coli strains that depend on biphenylalanine incorporation. Finally, we show that our posttranslational proofreading system can be designed for incorporation of other nsAAs by rational engineering of the ClpS protein, which mediates the N-end rule. Taken together, our posttranslational proofreading system for in vivo protein sequence verification presents an alternative paradigm for molecular recognition of amino acids and is a major advance in our ability to accurately expand the genetic code.
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18
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Pokhrel N, Origanti S, Davenport EP, Gandhi D, Kaniecki K, Mehl RA, Greene EC, Dockendorff C, Antony E. Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids. Nucleic Acids Res 2017; 45:9413-9426. [PMID: 28934470 PMCID: PMC5766198 DOI: 10.1093/nar/gkx598] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/09/2017] [Indexed: 12/23/2022] Open
Abstract
An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance.
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Affiliation(s)
- Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Sofia Origanti
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | | | - Disha Gandhi
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Kyle Kaniecki
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chris Dockendorff
- Department of Chemistry, Marquette University, Milwaukee, WI 53201, USA
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
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19
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Agostini F, Völler J, Koksch B, Acevedo‐Rocha CG, Kubyshkin V, Budisa N. Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology. Angew Chem Int Ed Engl 2017; 56:9680-9703. [DOI: 10.1002/anie.201610129] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/13/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Federica Agostini
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Jan‐Stefan Völler
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry—Organic ChemistryFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | | | - Vladimir Kubyshkin
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Nediljko Budisa
- Institut für ChemieTechnische Universität Berlin Müller-Breslau-Strasse 10 10623 Berlin Germany
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20
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Hauf M, Richter F, Schneider T, Faidt T, Martins BM, Baumann T, Durkin P, Dobbek H, Jacobs K, Möglich A, Budisa N. Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code. Chembiochem 2017. [DOI: 10.1002/cbic.201700327] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Matthias Hauf
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Florian Richter
- Institut für Biologie; Biophysikalische Chemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Germany
| | - Tobias Schneider
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Thomas Faidt
- Experimental Physics; Saarland University; Campus E2 9 66123 Saarbrücken Germany
| | - Berta M. Martins
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Germany
| | - Tobias Baumann
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Patrick Durkin
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Germany
| | - Karin Jacobs
- Experimental Physics; Saarland University; Campus E2 9 66123 Saarbrücken Germany
| | - Andreas Möglich
- Institut für Biologie; Biophysikalische Chemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Germany
- Lehrstuhl für Biochemie; Universität Bayreuth; Universitätsstrasse 30 95440 Bayreuth Germany
| | - Nediljko Budisa
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
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21
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Biokatalyse mit nicht‐natürlichen Aminosäuren: Enzymologie trifft Xenobiologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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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: 45] [Impact Index Per Article: 6.4] [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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23
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Gan Q, Fan C. Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis. Biochim Biophys Acta Gen Subj 2016; 1861:3047-3052. [PMID: 27919800 DOI: 10.1016/j.bbagen.2016.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/04/2016] [Accepted: 12/01/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. METHODS We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position. RESULTS By removing three near cognate tRNA isoacceptors of the amber stop codon [tRNALys, tRNATyr, and tRNAGln(CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved. CONCLUSIONS Removal of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems. GENERAL SIGNIFICANCE We provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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24
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Exner MP, Kuenzl T, To TMT, Ouyang Z, Schwagerus S, Hoesl MG, Hackenberger CPR, Lensen MC, Panke S, Budisa N. Design ofS-Allylcysteine in Situ Production and Incorporation Based on a Novel Pyrrolysyl-tRNA Synthetase Variant. Chembiochem 2016; 18:85-90. [DOI: 10.1002/cbic.201600537] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Matthias P. Exner
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Tilmann Kuenzl
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
| | - Tuyet Mai T. To
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Zhaofei Ouyang
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 124 10623 Berlin Germany
| | - Sergej Schwagerus
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 BerlinBuch Germany
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Michael G. Hoesl
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
| | - Christian P. R. Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Strasse 10 13125 BerlinBuch Germany
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marga C. Lensen
- Institut für Chemie; Technische Universität Berlin; Strasse des 17. Juni 124 10623 Berlin Germany
| | - Sven Panke
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Switzerland
| | - Nediljko Budisa
- Institut für Chemie; Technische Universität Berlin; Müller-Breslau-Strasse 10 10623 Berlin Germany
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25
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Towards Biocontained Cell Factories: An Evolutionarily Adapted Escherichia coli Strain Produces a New-to-nature Bioactive Lantibiotic Containing Thienopyrrole-Alanine. Sci Rep 2016; 6:33447. [PMID: 27634138 PMCID: PMC5025777 DOI: 10.1038/srep33447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/25/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic code engineering that enables reassignment of genetic codons to non-canonical amino acids (ncAAs) is a powerful strategy for enhancing ribosomally synthesized peptides and proteins with functions not commonly found in Nature. Here we report the expression of a ribosomally synthesized and post-translationally modified peptide (RiPP), the 32-mer lantibiotic lichenicidin with a canonical tryptophan (Trp) residue replaced by the ncAA L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) which does not sustain cell growth in the culture. We have demonstrated that cellular toxicity of [3,2]Tpa for the production of the new-to-nature bioactive congener of lichenicidin in the host Escherichia coli can be alleviated by using an evolutionarily adapted host strain MT21 which not only tolerates [3,2]Tpa but also uses it as a proteome-wide synthetic building block. This work underscores the feasibility of the biocontainment concept and establishes a general framework for design and large scale production of RiPPs with evolutionarily adapted host strains.
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26
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Yang ST, Lim SI, Kiessling V, Kwon I, Tamm LK. Site-specific fluorescent labeling to visualize membrane translocation of a myristoyl switch protein. Sci Rep 2016; 6:32866. [PMID: 27605302 PMCID: PMC5015116 DOI: 10.1038/srep32866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022] Open
Abstract
Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein's folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons. We demonstrate reversible Ca(2+)-responsive translocation of labeled recoverin to membranes and show that recoverin favors membranes with negative curvature and high lipid fluidity in complex heterogeneous membranes, which confers spatio-temporal control over down-stream signaling events. The site-specific orthogonal labeling technique is promising for structural, dynamical, and functional studies of many lipid-anchored membrane protein switches.
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Affiliation(s)
- Sung-Tae Yang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Sung In Lim
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Volker Kiessling
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, USA
- School of Materials Science and Engineering, and Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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27
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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28
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Maruani A, Richards DA, Chudasama V. Dual modification of biomolecules. Org Biomol Chem 2016; 14:6165-78. [PMID: 27278999 DOI: 10.1039/c6ob01010e] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With the advent of novel bioorthogonal reactions and "click" chemistry, an increasing number of strategies for the single labelling of proteins and oligonucleotides have emerged. Whilst several methods exist for the site-selective introduction of a single chemical moiety, site-selective and bioorthogonal dual modification of biomolecules remains a challenge. The introduction of multiple modules enables a plethora of permutations and combinations and can generate a variety of bioconjuguates with many potential applications. From de novo approaches on oligomers to the post-translational functionalisation of proteins, this review will highlight the main strategies to dually modify biomolecules.
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Affiliation(s)
- Antoine Maruani
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H OAJ, UK.
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29
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Incorporation of non-canonical amino acids into proteins in yeast. Fungal Genet Biol 2016; 89:137-156. [DOI: 10.1016/j.fgb.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
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30
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Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life. Life (Basel) 2016; 6:life6010012. [PMID: 26999216 PMCID: PMC4810243 DOI: 10.3390/life6010012] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.
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31
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Haney CM, Wissner RF, Warner JB, Wang YJ, Ferrie JJ, J Covell D, Karpowicz RJ, Lee VMY, Petersson EJ. Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis. Org Biomol Chem 2016; 14:1584-92. [PMID: 26695131 PMCID: PMC4733880 DOI: 10.1039/c5ob02329g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of the amyloidogenic Parkinson's disease protein α-synuclein (αS) has proven difficult due to its structural plasticity. Here, we present a number of complementary methods to site-specifically introduce fluorescent probes to examine αS fibril formation and cellular uptake. By using various combinations of conventional Cys modification, amber codon suppression, transferase mediated N-terminal modification, and native chemical ligation, several variants of singly- and doubly-labeled αS were produced. We validated the nonperturbative nature of the label by a combination of in vitro aggregation kinetics measurements and imaging of the resulting fibrils. The labeled αS can then be used to monitor conformational changes during fibril formation or cellular uptake of αS fibrils in models of disease propagation.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Rebecca F Wissner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John B Warner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Dustin J Covell
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Richard J Karpowicz
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
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32
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Shao N, Singh NS, Slade SE, Jones AME, Balasubramanian MK. Site Specific Genetic Incorporation of Azidophenylalanine in Schizosaccharomyces pombe. Sci Rep 2015; 5:17196. [PMID: 26597962 PMCID: PMC4657001 DOI: 10.1038/srep17196] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/02/2022] Open
Abstract
The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins.
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Affiliation(s)
- Nan Shao
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK CV4 7AL.,Department of Biological Sciences, National University of Singapore, Singapore 117543.,Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - N Sadananda Singh
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604
| | - Susan E Slade
- School of Life Sciences, University of Warwick, Coventry, UK CV4 7AL
| | | | - Mohan K Balasubramanian
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry, UK CV4 7AL.,Department of Biological Sciences, National University of Singapore, Singapore 117543.,Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Mechanobiology Institute, 5A Engineering Drive 1, National University of Singapore, Singapore 117411
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33
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Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, Isaacs FJ. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol 2015; 33:1272-1279. [PMID: 26571098 DOI: 10.1038/nbt.3372] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/11/2015] [Indexed: 01/24/2023]
Abstract
Expansion of the genetic code with nonstandard amino acids (nsAAs) has enabled biosynthesis of proteins with diverse new chemistries. However, this technology has been largely restricted to proteins containing a single or few nsAA instances. Here we describe an in vivo evolution approach in a genomically recoded Escherichia coli strain for the selection of orthogonal translation systems capable of multi-site nsAA incorporation. We evolved chromosomal aminoacyl-tRNA synthetases (aaRSs) with up to 25-fold increased protein production for p-acetyl-L-phenylalanine and p-azido-L-phenylalanine (pAzF). We also evolved aaRSs with tunable specificities for 14 nsAAs, including an enzyme that efficiently charges pAzF while excluding 237 other nsAAs. These variants enabled production of elastin-like-polypeptides with 30 nsAA residues at high yields (∼50 mg/L) and high accuracy of incorporation (>95%). This approach to aaRS evolution should accelerate and expand our ability to produce functionalized proteins and sequence-defined polymers with diverse chemistries.
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Affiliation(s)
- Miriam Amiram
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Adrian D Haimovich
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Chenguang Fan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Yane-Shih Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Hans-Rudolf Aerni
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Daniel W Moonan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Natalie J Ma
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Alexis J Rovner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Jesse Rinehart
- Systems Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA
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34
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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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35
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Tian H, Sakmar TP, Huber T. Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR. Chembiochem 2015; 16:1314-22. [PMID: 25962668 PMCID: PMC5287413 DOI: 10.1002/cbic.201500030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Genetically encoded p-azido-phenylalanine (azF) residues in G protein-coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne-modified (DIBO-modified) fluorescent probes by means of strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent-solubilized receptors exhibit up to 1000-fold rate enhancement relative to azF residues on water-exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle-enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge (Sweden).
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
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36
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Mühlberg M, Hoesl MG, Kuehne C, Dernedde J, Budisa N, Hackenberger CPR. Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds. Beilstein J Org Chem 2015; 11:784-791. [PMID: 26124880 PMCID: PMC4464295 DOI: 10.3762/bjoc.11.88] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/05/2015] [Indexed: 01/12/2023] Open
Abstract
To add new tools to the repertoire of protein-based multivalent scaffold design, we have developed a novel dual-labeling strategy for proteins that combines residue-specific incorporation of unnatural amino acids with chemical oxidative aldehyde formation at the N-terminus of a protein. Our approach relies on the selective introduction of two different functional moieties in a protein by mutually orthogonal copper-catalyzed azide-alkyne cycloaddition (CuAAC) and oxime ligation. This method was applied to the conjugation of biotin and β-linked galactose residues to yield an enzymatically active thermophilic lipase, which revealed specific binding to Erythrina cristagalli lectin by SPR binding studies.
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Affiliation(s)
- Michaela Mühlberg
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 3, 14195 Berlin, Germany
| | - Michael G Hoesl
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian Kuehne
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jens Dernedde
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nediljko Budisa
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian P R Hackenberger
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Institut für Organische und Bioorganische Chemie, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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37
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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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38
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Kuthning A, Mösker E, Süssmuth RD. Engineering the heterologous expression of lanthipeptides in Escherichia coli by multigene assembly. Appl Microbiol Biotechnol 2015; 99:6351-61. [PMID: 25846334 DOI: 10.1007/s00253-015-6557-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/13/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
Abstract
Lantibiotics are an important class of ribosomally synthesised peptide antibiotics with a remarkable pharmacological potential. Structural variants of lantibiotics generated by peptide engineering in vivo are an important aspect for improving the peptide's efficacy, stability and bioavailability as well as production titre, which severely impacts the potential exploitation in pharmaceutical applications. Therefore, expression systems are needed which allow for a robust genetic access for ample mutagenesis experiments. Based on previous heterologous expression of the two-component lanthipeptide lichenicidin (Bliα and Bliβ) in Escherichia coli BLic5, we now employ a multigene assembly strategy for recombinant lantibiotic peptide production in the Gram-negative host. Two E. coli high copy plasmids for separate and increased expression of a two-component lantibiotic were cloned and tested for expression. From these E. coli HP expression strains, an up to 100 times increased expression was found compared with Bacillus licheniformis I89 and E. coli BLic5. Total expression yields reach 4 mg L(-1) for Bliα and 6 mg L(-1) for Bliβ. The expression system developed in this study constitutes an important cornerstone for future in vivo peptide engineering studies and is of significance for potential applications aiming at higher production titres of ribosomally synthesised, post translationally modified peptides.
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Affiliation(s)
- Anja Kuthning
- Institut für Chemie, Technische Universität Berlin, Straße des 17 Juni 124, 10623, Berlin, Germany
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39
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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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40
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Hong SH, Ntai I, Haimovich AD, Kelleher NL, Isaacs FJ, Jewett MC. Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific nonstandard amino acid incorporation. ACS Synth Biol 2014; 3:398-409. [PMID: 24328168 PMCID: PMC4065633 DOI: 10.1021/sb400140t] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Site-specific incorporation of nonstandard
amino acids (NSAAs)
into proteins enables the creation of biopolymers, proteins, and enzymes
with new chemical properties, new structures, and new functions. To
achieve this, amber (TAG codon) suppression has been widely applied.
However, the suppression efficiency is limited due to the competition
with translation termination by release factor 1 (RF1), which leads
to truncated products. Recently, we constructed a genomically recoded Escherichia coli strain lacking RF1 where 13 occurrences
of the amber stop codon have been reassigned to the synonymous TAA
codon (rEc.E13.ΔprfA). Here, we assessed and
characterized cell-free protein synthesis (CFPS) in crude S30 cell
lysates derived from this strain. We observed the synthesis of 190
± 20 μg/mL of modified soluble superfolder green fluorescent
protein (sfGFP) containing a single p-propargyloxy-l-phenylalanine (pPaF) or p-acetyl-l-phenylalanine. As compared to the parent rEc.E13 strain with RF1, this results in a modified sfGFP synthesis improvement
of more than 250%. Beyond introducing a single NSAA, we further demonstrated
benefits of CFPS from the RF1-deficient strains for incorporating
pPaF at two- and five-sites per sfGFP protein. Finally, we compared
our crude S30 extract system to the PURE translation system lacking
RF1. We observed that our S30 extract based approach is more cost-effective
and high yielding than the PURE translation system lacking RF1, ∼1000
times on a milligram protein produced/$ basis. Looking forward, using
RF1-deficient strains for extract-based CFPS will aid in the synthesis
of proteins and biopolymers with site-specifically incorporated NSAAs.
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Affiliation(s)
| | | | - Adrian D. Haimovich
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States of America
- Systems Biology
Institute, Yale University, West Haven, Connecticut 06516, United States of America
| | - Neil L. Kelleher
- Member,
Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States of America
| | - Farren J. Isaacs
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States of America
- Systems Biology
Institute, Yale University, West Haven, Connecticut 06516, United States of America
| | - Michael C. Jewett
- Member,
Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States of America
- Institute
of Bionanotechnology in Medicine, Northwestern University, Chicago, Illinois 60611, United States of America
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41
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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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42
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An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins. J Biotechnol 2014; 178:12-22. [DOI: 10.1016/j.jbiotec.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/08/2014] [Accepted: 02/14/2014] [Indexed: 11/19/2022]
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An in vivo photo-cross-linking approach reveals a homodimerization domain of Aha1 in S. cerevisiae. PLoS One 2014; 9:e89436. [PMID: 24614167 PMCID: PMC3948627 DOI: 10.1371/journal.pone.0089436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 01/23/2014] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions play an essential role in almost any biological processes. Therefore, there is a particular need for methods which describe the interactions of a defined target protein in its physiological context. Here we report a method to photo-cross-link interacting proteins in S. cerevisiae by using the non-canonical amino acid p-azido-L-phenylalanine (pAzpa). Based on the expanded genetic code the photoreactive non-canonical amino acid pAzpa was site-specifically incorporated at eight positions into a domain of Aha1 that was previously described to bind Hsp90 in vitro to function as a cochaperone of Hsp90 and activates its ATPase activity. In vivo photo-cross-linking to the cognate binding partner of Aha1 was carried out by irradiation of mutant strains with UV light (365 nm) to induce covalent intermolecular bonds. Surprisingly, an interaction between Aha1 and Hsp90 was not detected, although, we could confirm binding of suppressed pAzpa containing Aha1 to Hsp90 by native co-immunoprecipitation. However, a homodimer consisting of two covalently crosslinked Aha1 monomers was identified by mass spectrometry. This homodimer could also be confirmed using p-benzoyl-L-phenylalanine, another photoreactive non-canonical amino acid. Crosslinking was highly specific as it was dependent on irradiation using UV light, the exact position of the non-canonical amino acid in the protein sequence as well as on the addition of the non-canonical amino acid to the growth medium. Therefore it seems possible that an interaction of Aha1 with Hsp90 takes place at different positions than previously described in vitro highlighting the importance of in vivo techniques to study protein-protein interactions. Accordingly, the expanded genetic code can easily be applied to other S. cerevisiae proteins to study their interaction under physiological relevant conditions in vivo.
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Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C, Glass JI, Rinehart J, Söll D. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem 2013; 14:1967-72. [PMID: 24000185 DOI: 10.1002/cbic.201300444] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Indexed: 12/22/2022]
Abstract
Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused (or rarely used) codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. The Mycoplasma capricolum genome contains just six CGG arginine codons, without a dedicated tRNA(Arg). We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNA(Pyl)(CCG)), and the genes for pyrrolysine biosynthesis. Here we show that tRNA(Pyl)(CCG) is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of tRNA(Pyl)(CCG), CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding.
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Affiliation(s)
- Radha Krishnakumar
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 (USA)
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45
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Nathani RI, Moody P, Chudasama V, Smith MEB, Fitzmaurice RJ, Caddick S. A novel approach to the site-selective dual labelling of a protein via chemoselective cysteine modification. Chem Sci 2013; 4:3455-3458. [PMID: 24741436 PMCID: PMC3985185 DOI: 10.1039/c3sc51333e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/17/2013] [Indexed: 11/21/2022] Open
Abstract
Local protein microenvironment is used to control the outcome of reaction between cysteine residues and 2,5-dibromohexanediamide. The differential reactivity is exploited to introduce two orthogonal reactive handles onto the surface of a double cysteine mutant of superfolder green fluorescent protein in a regioselective manner. Subsequent elaboration with commonly used thiol and alkyne containing reagents affects site-selective protein dual labelling.
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Affiliation(s)
- Ramiz I Nathani
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
| | - Paul Moody
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
| | - Vijay Chudasama
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
| | - Mark E B Smith
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
| | - Richard J Fitzmaurice
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
| | - Stephen Caddick
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; ; Tel: +44 (0)20 3108 5071
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46
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Rupp S. Next-generation bioproduction systems: Cell-free conversion concepts for industrial biotechnology. Eng Life Sci 2013. [DOI: 10.1002/elsc.201100237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Steffen Rupp
- Department of Molecular Biotechnology; Fraunhofer IGB; Stuttgart; Germany
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Perona JJ, Hadd A. Structural diversity and protein engineering of the aminoacyl-tRNA synthetases. Biochemistry 2012; 51:8705-29. [PMID: 23075299 DOI: 10.1021/bi301180x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are the enzymes that ensure faithful transmission of genetic information in all living cells, and are central to the developing technologies for expanding the capacity of the translation apparatus to incorporate nonstandard amino acids into proteins in vivo. The 24 known aaRS families are divided into two classes that exhibit functional evolutionary convergence. Each class features an active site domain with a common fold that binds ATP, the amino acid, and the 3'-terminus of tRNA, embellished by idiosyncratic further domains that bind distal portions of the tRNA and enhance specificity. Fidelity in the expression of the genetic code requires that the aaRS be selective for both amino acids and tRNAs, a substantial challenge given the presence of structurally very similar noncognate substrates of both types. Here we comprehensively review central themes concerning the architectures of the protein structures and the remarkable dual-substrate selectivities, with a view toward discerning the most important issues that still substantially limit our capacity for rational protein engineering. A suggested general approach to rational design is presented, which should yield insight into the identities of the protein-RNA motifs at the heart of the genetic code, while also offering a basis for improving the catalytic properties of engineered tRNA synthetases emerging from genetic selections.
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Affiliation(s)
- John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States.
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O'Donoghue P, Prat L, Heinemann IU, Ling J, Odoi K, Liu WR, Söll D. Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion. FEBS Lett 2012; 586:3931-7. [PMID: 23036644 DOI: 10.1016/j.febslet.2012.09.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to 'statistical protein' that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNA(Pyl) orthogonal pair cannot completely outcompete contamination by natural amino acids.
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Affiliation(s)
- Patrick O'Donoghue
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
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