1
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Rozhoňová H, Martí-Gómez C, McCandlish DM, Payne JL. Robust genetic codes enhance protein evolvability. PLoS Biol 2024; 22:e3002594. [PMID: 38754362 PMCID: PMC11098591 DOI: 10.1371/journal.pbio.3002594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024] Open
Abstract
The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability-the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively.
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Affiliation(s)
- Hana Rozhoňová
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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2
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Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023; 62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Incorporation of more than one noncanonical amino acid (ncAA) within a single protein endows the resulting construct with multiple useful features such as augmented molecular recognition or covalent cross-linking capabilities. Herein, for the first time, we demonstrate the incorporation of two chemically distinct ncAAs into proteins biosynthesized in Saccharomyces cerevisiae. To complement ncAA incorporation in response to the amber (TAG) stop codon in yeast, we evaluated opal (TGA) stop codon suppression using three distinct orthogonal translation systems. We observed selective TGA readthrough without detectable cross-reactivity from host translation components. Readthrough efficiency at TGA was modulated by factors including the local nucleotide environment, gene deletions related to the translation process, and the identity of the suppressor tRNA. These observations facilitated systematic investigation of dual ncAA incorporation in both intracellular and yeast-displayed protein constructs, where we observed efficiencies up to 6% of wild-type protein controls. The successful display of doubly substituted proteins enabled the exploration of two critical applications on the yeast surface─(A) antigen binding functionality and (B) chemoselective modification with two distinct chemical probes through sequential application of two bioorthogonal click chemistry reactions. Lastly, by utilizing a soluble form of a doubly substituted construct, we validated the dual incorporation system using mass spectrometry and demonstrated the feasibility of conducting selective labeling of the two ncAAs sequentially using a "single-pot" approach. Overall, our work facilitates the addition of a 22nd amino acid to the genetic code of yeast and expands the scope of applications of ncAAs for basic biological research and drug discovery.
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Affiliation(s)
- Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Meghan S. Martin
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Rebecca A. Scheck
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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3
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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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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Edelstein EK, Rankic DA, Dudley CC, McMinn SE, Adpressa DA. Synthesis of Proline Analogues via Rh-Catalyzed Asymmetric Conjugate Addition. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Emma K. Edelstein
- Department of Process Research and Development, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Danica A. Rankic
- Department of Process Research and Development, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Caroline C. Dudley
- Department of Process Research and Development, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Spencer E. McMinn
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Donovon A. Adpressa
- Department of Process Research and Development, Merck & Co., Inc., Boston, Massachusetts 02115, United States
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6
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Sandanaraj BS, Bhandari PJ, Reddy MM, Lohote AB, Sahoo B. Design, Synthesis, and Self‐Assembly Studies of a Suite of Monodisperse, Facially Amphiphilic, Protein–Dendron Conjugates. Chembiochem 2019; 21:408-416. [DOI: 10.1002/cbic.201900341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Britto S. Sandanaraj
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | | | - Mullapudi Mohan Reddy
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | - Akshay Bhagwan Lohote
- Departments of Chemistry & BiologyIndian Institute of Science Education and Research (IISER) Pune 411 008 India
| | - Bankanidhi Sahoo
- Tata Institute of Fundamental Research Hyderabad (TIFR Hyd) Hyderabad 500019 India
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7
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Jin X, Park OJ, Hong SH. Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications. Appl Microbiol Biotechnol 2019; 103:2947-2958. [PMID: 30790000 PMCID: PMC6449208 DOI: 10.1007/s00253-019-09690-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022]
Abstract
The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
- Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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8
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Venkat S, Chen H, Gan Q, Fan C. The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications. Front Pharmacol 2019; 10:248. [PMID: 30949051 PMCID: PMC6436179 DOI: 10.3389/fphar.2019.00248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/26/2019] [Indexed: 02/04/2023] Open
Abstract
The translation system is a sophisticated machinery that synthesizes proteins from 20 canonical amino acids. Recently, the repertoire of such composition has been expanded by the introduction of non-canonical amino acids (ncAAs) with the genetic code expansion strategy, which provides proteins with designed properties and structures for protein studies and engineering. Although the genetic code expansion strategy has been mostly implemented by using living cells as the host, a number of limits such as poor cellular uptake or solubility of specific ncAA substrates and the toxicity of target proteins have hindered the production of certain ncAA-modified proteins. To overcome those challenges, cell-free protein synthesis (CFPS) has been applied as it allows the precise control of reaction components. Several approaches have been recently developed to increase the purity and efficiency of ncAA incorporation in CFPS. Here, we summarized recent development of CFPS with an emphasis on its applications in generating site-specific protein post-translational modifications by the genetic code expansion strategy.
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Affiliation(s)
- Sumana Venkat
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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9
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Chen H, Venkat S, McGuire P, Gan Q, Fan C. Recent Development of Genetic Code Expansion for Posttranslational Modification Studies. Molecules 2018; 23:E1662. [PMID: 29986538 PMCID: PMC6100177 DOI: 10.3390/molecules23071662] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022] Open
Abstract
Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Sumana Venkat
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Paige McGuire
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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10
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Kwon I, Yang B. Bioconjugation and Active Site Design of Enzymes Using Non-natural Amino Acids. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b00612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Inchan Kwon
- School
of Materials Science and Engineering (SMSE) and ‡Department of Biomedical Science
and Engineering (BMSE), Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Byungseop Yang
- School
of Materials Science and Engineering (SMSE) and ‡Department of Biomedical Science
and Engineering (BMSE), Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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11
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Gan Q, Lehman BP, Bobik TA, Fan C. Expanding the genetic code of Salmonella with non-canonical amino acids. Sci Rep 2016; 6:39920. [PMID: 28008993 PMCID: PMC5180212 DOI: 10.1038/srep39920] [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: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Brent P Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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12
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Hammerling MJ, Gollihar J, Mortensen C, Alnahhas RN, Ellington AD, Barrick JE. Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance inEscherichia coli. Mol Biol Evol 2016; 33:2054-63. [DOI: 10.1093/molbev/msw094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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13
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Cachat E, Liu W, Martin KC, Yuan X, Yin H, Hohenstein P, Davies JA. 2- and 3-dimensional synthetic large-scale de novo patterning by mammalian cells through phase separation. Sci Rep 2016; 6:20664. [PMID: 26857385 PMCID: PMC4746622 DOI: 10.1038/srep20664] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/11/2016] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology provides an opportunity for the construction and exploration of alternative solutions to biological problems - solutions different from those chosen by natural life. To this end, synthetic biologists have built new sensory systems, cellular memories, and alternative genetic codes. There is a growing interest in applying synthetic approaches to multicellular systems, especially in relation to multicellular self-organization. Here we describe a synthetic biological system that confers large-scale de novo patterning activity on 2-D and 3-D populations of mammalian cells. Instead of using the reaction-diffusion mechanisms common in real embryos, our system uses cadherin-mediated phase separation, inspired by the known phenomenon of cadherin-based sorting. An engineered self-organizing, large-scale patterning system requiring no prior spatial cue may be a significant step towards the construction of self-assembling synthetic tissues.
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Affiliation(s)
- Elise Cachat
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Weijia Liu
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Kim C. Martin
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK
| | - Xiaofei Yuan
- School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
| | - Huabing Yin
- School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
| | - Peter Hohenstein
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jamie A. Davies
- Centre for Integrative Physiology & Synthsys Centre for Synthetic & Systems Biology, University of Edinburgh, George Square, Edinburgh EH8 9XB, UK,
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14
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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15
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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: 188] [Impact Index Per Article: 20.9] [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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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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Moatsou D, Li J, Ranji A, Pitto-Barry A, Ntai I, Jewett MC, O’Reilly RK. Self-Assembly of Temperature-Responsive Protein-Polymer Bioconjugates. Bioconjug Chem 2015; 26:1890-9. [PMID: 26083370 PMCID: PMC4577958 DOI: 10.1021/acs.bioconjchem.5b00264] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/12/2015] [Indexed: 12/13/2022]
Abstract
We report a simple temperature-responsive bioconjugate system comprising superfolder green fluorescent protein (sfGFP) decorated with poly[(oligo ethylene glycol) methyl ether methacrylate] (PEGMA) polymers. We used amber suppression to site-specifically incorporate the non-canonical azide-functional amino acid p-azidophenylalanine (pAzF) into sfGFP at different positions. The azide moiety on modified sfGFP was then coupled using copper-catalyzed "click" chemistry with the alkyne terminus of a PEGMA synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. The protein in the resulting bioconjugate was found to remain functionally active (i.e., fluorescent) after conjugation. Turbidity measurements revealed that the point of attachment of the polymer onto the protein scaffold has an impact on the thermoresponsive behavior of the resultant bioconjugate. Furthermore, small-angle X-ray scattering analysis showed the wrapping of the polymer around the protein in a temperature-dependent fashion. Our work demonstrates that standard genetic manipulation combined with an expanded genetic code provides an easy way to construct functional hybrid biomaterials where the location of the conjugation site on the protein plays an important role in determining material properties. We anticipate that our approach could be generalized for the synthesis of complex functional materials with precisely defined domain orientation, connectivity, and composition.
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Affiliation(s)
- Dafni Moatsou
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Jian Li
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Arnaz Ranji
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Anaïs Pitto-Barry
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Ioanna Ntai
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
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Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
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Hong SH, Kwon YC, Martin RW, Des Soye BJ, de Paz AM, Swonger KN, Ntai I, Kelleher NL, Jewett MC. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. Chembiochem 2015; 16:844-53. [PMID: 25737329 DOI: 10.1002/cbic.201402708] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/12/2022]
Abstract
Site-specific incorporation of non-standard amino acids (NSAAs) into proteins opens the way to novel biological insights and applications in biotechnology. Here, we describe the development of a high yielding cell-free protein synthesis (CFPS) platform for NSAA incorporation from crude extracts of genomically recoded Escherichia coli lacking release factor 1. We used genome engineering to construct synthetic organisms that, upon cell lysis, lead to improved extract performance. We targeted five potential negative effectors to be disabled: the nuclease genes rna, rnb, csdA, mazF, and endA. Using our most productive extract from strain MCJ.559 (csdA(-) endA(-)), we synthesized 550±40 μg mL(-1) of modified superfolder green fluorescent protein containing p-acetyl-L-phenylalanine. This yield was increased to ∼1300 μg mL(-1) when using a semicontinuous method. Our work has implications for using whole genome editing for CFPS strain development, expanding the chemistry of biological systems, and cell-free synthetic biology.
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Affiliation(s)
- Seok Hoon Hong
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208 (USA)
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