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Volkwein W, Maier C, Krafczyk R, Jung K, Lassak J. A Versatile Toolbox for the Control of Protein Levels Using N ε-Acetyl-l-lysine Dependent Amber Suppression. ACS Synth Biol 2017; 6:1892-1902. [PMID: 28594177 DOI: 10.1021/acssynbio.7b00048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The analysis of the function of essential genes in vivo depends on the ability to experimentally modulate levels of their protein products. Current methods to address this are based on transcriptional or post-transcriptional regulation of mRNAs, but approaches based on the exploitation of translation regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of Nε-acetyl-l-lysine (AcK), for translational tuning of protein output. We chose the highly sensitive luminescence system LuxCDABE as a reporter and incorporated a UAG stop codon into the gene for the reductase subunit LuxC. The system was used to measure and compare the effects of AcK- and Nε-(tert-butoxycarbonyl)-l-lysine (BocK) dependent amber suppression in Escherichia coli. We also demonstrate here that, in combination with transcriptional regulation, the system allows protein production to be either totally repressed or gradually adjusted. To identify sequence motifs that provide improved translational regulation, we varied the sequence context of the amber codon and found that insertion of two preceding prolines drastically decreases luminescence. In addition, using LacZ as a reporter, we demonstrated that a strain encoding a variant with a Pro-Pro amber motif can only grow on lactose when AcK is supplied, thus confirming the tight translational regulation of protein output. In parallel, we constructed an E. coli strain that carries an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible version of the AcK-tRNA synthetase (AcKRS) gene on the chromosome, thus preventing mischarging of noncognate substrates. Subsequently, a diaminopimelic acid auxotrophic mutant (ΔdapA) was generated demonstrating the potential of this strain in regulating essential gene products. Furthermore, we assembled a set of vectors based on the broad-host-range pBBR ori that enable the AcK-dependent amber suppression system to control protein output not only in E. coli, but also in Salmonella enterica and Vibrio cholerae.
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Affiliation(s)
- Wolfram Volkwein
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Christopher Maier
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Ralph Krafczyk
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Jürgen Lassak
- Center for integrated Protein
Science Munich (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
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52
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Repurposing ribosomes for synthetic biology. Curr Opin Chem Biol 2017; 40:87-94. [PMID: 28869851 DOI: 10.1016/j.cbpa.2017.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
Abstract
The translation system is the cell's factory for protein biosynthesis, stitching together hundreds to thousands of amino acids into proteins, which are required for the structure, function, and regulation of living systems. The extraordinary synthetic capability of this system, which includes the ribosome and its associated factors required for polymerization, has driven extensive efforts to harness it for societal use in areas as diverse as energy, materials, and medicine. A powerful example is recombinant protein production, which has impacted the lives of patients through the synthesis of biopharmaceuticals such as insulin. In nature, however, only limited sets of monomers are utilized, thereby resulting in limited sets of biopolymers (i.e., proteins). Expanding nature's repertoire of ribosomal monomers could yield new classes of enzymes, therapeutics, materials, and chemicals with diverse, genetically encoded chemistry. Here, we discuss recent progress towards engineering ribosomes both in vivo and in vitro. These fundamental and technical breakthroughs open doors for advanced applications in biotechnology and synthetic biology.
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53
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Rustad M, Eastlund A, Marshall R, Jardine P, Noireaux V. Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System. J Vis Exp 2017. [PMID: 28872145 DOI: 10.3791/56144] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits. In vitro TXTL has proven convenient to rapidly prototype regulatory elements and biological networks as well as to recapitulate molecular self-assembly mechanisms found in living systems. In this article, we describe how infectious bacteriophages, such as MS2 (RNA), ΦΧ174 (ssDNA), and T7 (dsDNA), are entirely synthesized from their genome in one-pot reactions using an all Escherichia coli, cell-free TXTL system. Synthesis of the three coliphages is quantified using the plaque assay. We show how the yield of synthesized phage depends on the biochemical settings of the reactions. Molecular crowding, emulated through a controlled concentration of PEG 8000, affects the amount of synthesized phages by orders of magnitudes. We also describe how to amplify the phages and how to purify their genomes. The set of protocols and results presented in this work should be of interest to multidisciplinary researchers involved in cell-free synthetic biology and bioengineering.
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Affiliation(s)
- Mark Rustad
- School of Physics and Astronomy, University of Minnesota
| | - Allen Eastlund
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota
| | - Paul Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota
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54
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Chernoff N, Hill DJ, Diggs DL, Faison BD, Francis BM, Lang JR, Larue MM, Le TT, Loftin KA, Lugo JN, Schmid JE, Winnik WM. A critical review of the postulated role of the non-essential amino acid, β-N-methylamino-L-alanine, in neurodegenerative disease in humans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2017; 20:1-47. [PMID: 28598725 PMCID: PMC6503681 DOI: 10.1080/10937404.2017.1297592] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The compound BMAA (β-N-methylamino-L-alanine) has been postulated to play a significant role in four serious neurological human diseases: Amyotrophic Lateral Sclerosis/Parkinsonism Dementia Complex (ALS/PDC) found on Guam, and ALS, Parkinsonism, and dementia that occur globally. ALS/PDC with symptoms of all three diseases first came to the attention of the scientific community during and after World War II. It was initially associated with cycad flour used for food because BMAA is a product of symbiotic cycad root-dwelling cyanobacteria. Human consumption of flying foxes that fed on cycad seeds was later suggested as a source of BMAA on Guam and a cause of ALS/PDC. Subsequently, the hypothesis was expanded to include a causative role for BMAA in other neurodegenerative diseases including Alzheimer's disease (AD) through exposures attributed to proximity to freshwaters and/or consumption of seafood due to its purported production by most species of cyanobacteria. The hypothesis that BMAA is the critical factor in the genesis of these neurodegenerative diseases received considerable attention in the medical, scientific, and public arenas. This review examines the history of ALS/PDC and the BMAA-human disease hypotheses; similarities and differences between ALS/PDC and the other diseases with similar symptomologies; the relationship of ALS/PDC to other similar diseases, studies of BMAA-mediated effects in lab animals, inconsistencies and data gaps in the hypothesis; and other compounds and agents that were suggested as the cause of ALS/PDC on Guam. The review concludes that the hypothesis of a causal BMAA neurodegenerative disease relationship is not supported by existing data.
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Affiliation(s)
- N. Chernoff
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - D. J. Hill
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - D. L. Diggs
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - B. D. Faison
- U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, Washington, DC, USA
| | - B. M. Francis
- Department of Entomology, University of Illinois, Champaign-Urbana, IL, USA
| | - J. R Lang
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - M. M. Larue
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | - T.-T. Le
- Oak Ridge Institute for Science and Education Internship/Research Participation Program at the U.S. Environmental Protection Agency, NHEERL, Research Triangle Park, NC, USA
| | | | - J. N. Lugo
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
| | - J. E. Schmid
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
| | - W. M. Winnik
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC, USA
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55
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Yin G, Stephenson HT, Yang J, Li X, Armstrong SM, Heibeck TH, Tran C, Masikat MR, Zhou S, Stafford RL, Yam AY, Lee J, Steiner AR, Gill A, Penta K, Pollitt S, Baliga R, Murray CJ, Thanos CD, McEvoy LM, Sato AK, Hallam TJ. RF1 attenuation enables efficient non-natural amino acid incorporation for production of homogeneous antibody drug conjugates. Sci Rep 2017; 7:3026. [PMID: 28596531 PMCID: PMC5465077 DOI: 10.1038/s41598-017-03192-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/27/2017] [Indexed: 11/12/2022] Open
Abstract
Amber codon suppression for the insertion of non-natural amino acids (nnAAs) is limited by competition with release factor 1 (RF1). Here we describe the genome engineering of a RF1 mutant strain that enhances suppression efficiency during cell-free protein synthesis, without significantly impacting cell growth during biomass production. Specifically, an out membrane protease (OmpT) cleavage site was engineered into the switch loop of RF1, which enables its conditional inactivation during cell lysis. This facilitates extract production without additional processing steps, resulting in a scaleable extract production process. The RF1 mutant extract allows nnAA incorporation at previously intractable sites of an IgG1 and at multiple sites in the same polypeptide chain. Conjugation of cytotoxic agents to these nnAAs, yields homogeneous antibody drug conjugates (ADCs) that can be optimized for conjugation site, drug to antibody ratio (DAR) and linker-warheads designed for efficient tumor killing. This platform provides the means to generate therapeutic ADCs inaccessible by other methods that are efficient in their cytotoxin delivery to tumor with reduced dose-limiting toxicities and thus have the potential for better clinical impact.
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Affiliation(s)
- Gang Yin
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA.
| | | | - Junhao Yang
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Xiaofan Li
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | | | - Cuong Tran
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Sihong Zhou
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Alice Y Yam
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - John Lee
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | - Avinash Gill
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Kalyani Penta
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Sonia Pollitt
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | - Ramesh Baliga
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
| | | | | | | | - Aaron K Sato
- Sutro Biopharma Inc, South San Francisco, CA, 94080, USA
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56
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Novel DNA/RNA-targeting amino acid beacon for the versatile incorporation at any position within the peptide backbone. Amino Acids 2017; 49:1381-1388. [DOI: 10.1007/s00726-017-2438-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 01/28/2023]
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57
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58
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Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol Bioeng 2017; 114:1074-1086. [PMID: 27987323 DOI: 10.1002/bit.26239] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/28/2016] [Accepted: 12/13/2016] [Indexed: 01/15/2023]
Abstract
The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120
| | - Ioanna Ntai
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208-0001.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208.,Simpson Querry Institute, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
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59
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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: 18] [Impact Index Per Article: 2.3] [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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60
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Legastelois I, Buffin S, Peubez I, Mignon C, Sodoyer R, Werle B. Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules. Hum Vaccin Immunother 2016; 13:947-961. [PMID: 27905833 DOI: 10.1080/21645515.2016.1260795] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids.
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Affiliation(s)
| | - Sophie Buffin
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | - Isabelle Peubez
- a Research and Development, Sanofi Pasteur , Marcy L'Etoile , France
| | | | - Régis Sodoyer
- b Technology Research Institute Bioaster , Lyon , France
| | - Bettina Werle
- b Technology Research Institute Bioaster , Lyon , France
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61
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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62
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Ozer E, Chemla Y, Schlesinger O, Aviram HY, Riven I, Haran G, Alfonta L. In vitro suppression of two different stop codons. Biotechnol Bioeng 2016; 114:1065-1073. [DOI: 10.1002/bit.26226] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/22/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Eden Ozer
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Yonatan Chemla
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Orr Schlesinger
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
| | - Haim Yuval Aviram
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Inbal Riven
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Gilad Haran
- Department of Chemical Physics; Weizmann Institute of Science; Rehovot Israel
| | - Lital Alfonta
- Department of Life Sciences and Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; P. O. Box 653 Beer-Sheva 84105 Israel
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63
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Thoring L, Wüstenhagen DA, Borowiak M, Stech M, Sonnabend A, Kubick S. Cell-Free Systems Based on CHO Cell Lysates: Optimization Strategies, Synthesis of "Difficult-to-Express" Proteins and Future Perspectives. PLoS One 2016; 11:e0163670. [PMID: 27684475 PMCID: PMC5042383 DOI: 10.1371/journal.pone.0163670] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/11/2016] [Indexed: 11/18/2022] Open
Abstract
Nowadays, biotechnological processes play a pivotal role in target protein production. In this context, Chinese Hamster Ovary (CHO) cells are one of the most prominent cell lines for the expression of recombinant proteins and revealed as a safe host for nearly 40 years. Nevertheless, the major bottleneck of common in vivo protein expression platforms becomes obvious when looking at the production of so called “difficult-to-express” proteins. This class of proteins comprises in particular several ion channels and multipass membrane proteins as well as cytotoxic proteins. To enhance the production of “difficult-to-express” proteins, alternative technologies were developed, mainly based on translationally active cell lysates. These so called “cell-free” protein synthesis systems enable an efficient production of different classes of proteins. Eukaryotic cell-free systems harboring endogenous microsomal structures for the synthesis of functional membrane proteins and posttranslationally modified proteins are of particular interest for future applications. Therefore, we present current developments in cell-free protein synthesis based on translationally active CHO cell extracts, underlining the high potential of this platform. We present novel results highlighting the optimization of protein yields, the synthesis of various “difficult-to-express” proteins and the cotranslational incorporation of non-standard amino acids, which was exemplarily demonstrated by residue specific labeling of the glycoprotein Erythropoietin and the multimeric membrane protein KCSA.
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Affiliation(s)
- Lena Thoring
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Doreen A. Wüstenhagen
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Maria Borowiak
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Marlitt Stech
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Andrei Sonnabend
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Stefan Kubick
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- * E-mail:
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64
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Focke PJ, Hein C, Hoffmann B, Matulef K, Bernhard F, Dötsch V, Valiyaveetil FI. Combining in Vitro Folding with Cell Free Protein Synthesis for Membrane Protein Expression. Biochemistry 2016; 55:4212-9. [PMID: 27384110 DOI: 10.1021/acs.biochem.6b00488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell free protein synthesis (CFPS) has emerged as a promising methodology for protein expression. While polypeptide production is very reliable and efficient using CFPS, the correct cotranslational folding of membrane proteins during CFPS is still a challenge. In this contribution, we describe a two-step protocol in which the integral membrane protein is initially expressed by CFPS as a precipitate followed by an in vitro folding procedure using lipid vesicles for converting the protein precipitate to the correctly folded protein. We demonstrate the feasibility of using this approach for the K(+) channels KcsA and MVP and the amino acid transporter LeuT. We determine the crystal structure of the KcsA channel obtained by CFPS and in vitro folding to show the structural similarity to the cellular expressed KcsA channel and to establish the feasibility of using this two-step approach for membrane protein production for structural studies. Our studies show that the correct folding of these membrane proteins with complex topologies can take place in vitro without the involvement of the cellular machinery for membrane protein biogenesis. This indicates that the folding instructions for these complex membrane proteins are contained entirely within the protein sequence.
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Affiliation(s)
- Paul J Focke
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Christopher Hein
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University , Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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Lee KH, Catherine C, Kim DM. Enhanced production of unnatural amino acid-containing proteins in a cell-free protein synthesis system. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2016.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Garamella J, Marshall R, Rustad M, Noireaux V. The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology. ACS Synth Biol 2016; 5:344-55. [PMID: 26818434 DOI: 10.1021/acssynbio.5b00296] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report on and provide a detailed characterization of the performance and properties of a recently developed, all Escherichia coli, cell-free transcription and translation system. Gene expression is entirely based on the endogenous translation components and transcription machinery provided by an E. coli cytoplasmic extract, thus expanding the repertoire of regulatory parts to hundreds of elements. We use a powerful metabolism for ATP regeneration to achieve more than 2 mg/mL of protein synthesis in batch mode reactions, and more than 6 mg/mL in semicontinuous mode. While the strength of cell-free expression is increased by a factor of 3 on average, the output signal of simple gene circuits and the synthesis of entire bacteriophages are increased by orders of magnitude compared to previous results. Messenger RNAs and protein degradation, respectively tuned using E. coli MazF interferase and ClpXP AAA+ proteases, are characterized over a much wider range of rates than the first version of the cell-free toolbox. This system is a highly versatile cell-free platform to construct complex biological systems through the execution of DNA programs composed of synthetic and natural bacterial regulatory parts.
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Affiliation(s)
- Jonathan Garamella
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Ryan Marshall
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Mark Rustad
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
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67
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Schoborg JA, Clark LG, Choudhury A, Hodgman CE, Jewett MC. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synth Syst Biotechnol 2016; 1:2-6. [PMID: 29062921 PMCID: PMC5640588 DOI: 10.1016/j.synbio.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems from crude lysates have benefitted from modifications to their enzyme composition. For example, functionally deleting enzymes in the source strain that are deleterious to CFPS can improve protein synthesis yields. However, making such modifications can take substantial time. As a proof-of-concept to accelerate prototyping capabilities, we assessed the feasibility of using the yeast knockout collection to identify negative effectors in a Saccharomyces cerevisiae CFPS platform. We analyzed extracts made from six deletion strains that targeted the single deletion of potentially negative effectors (e.g., nucleases). We found a statistically significant increase in luciferase yields upon loss of function of GCN3, PEP4, PPT1, NGL3, and XRN1 with a maximum increase of over 6-fold as compared to the wild type. Our work has implications for yeast CFPS and for rapidly prototyping strains to enable cell-free synthetic biology applications.
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Key Words
- ANOVA, analysis of variance
- ATP, adenosine triphosphate
- CFPS, cell-free protein synthesis
- CRISPR, clustered regularly interspaced short palindromic repeats
- Cell-free biology
- Cell-free protein synthesis
- In vitro translation
- NTP, nucleoside triphosphate
- OD, optical density
- Protein expression
- SC, synthetic complete media
- Saccharomyces cerevisiae
- Synthetic biology
- YKO, yeast knockout
- cAMP, cyclic adenosine monophosphate
- eIF, eukaryotic initiation factor
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Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
| | - C. Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
- Simpson Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131, Chicago, IL 60611-2875, USA
- Corresponding author. 2145 Sheridan Road, Tech E-136, Evanston, IL 60208-3120, USA.2145 Sheridan RoadTech E-136EvanstonIL60208-3120USA
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68
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Gan R, Jewett MC. Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnol Bioeng 2016; 113:1777-86. [PMID: 26757179 DOI: 10.1002/bit.25933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/13/2015] [Accepted: 01/07/2016] [Indexed: 11/08/2022]
Abstract
We report a novel in vitro yeast ribosome display method based on cell-free protein synthesis (CFPS) using linear DNA templates. We demonstrate that our platform can enrich a target gene from a model library by 100-fold per round of selection. We demonstrate the utility of our approach by evolving cap-independent translation initiation (CITI) sequences, which result in a 13-fold increase in CFPS yields after four rounds of selection, and a threefold further increase by placing the beneficial short sequences in tandem. We also show that 12 of the selected CITI sequences permit precise control of gene expression in vitro over a range of up to 80-fold by enhancing translation (and not as cryptic promoters). These 12 sequences are then shown to tune protein expression in vivo, though likely due to a different mechanism. Looking forward, yeast ribosome display holds promise for evolving libraries of proteins and DNA regulatory parts for protein engineering and synthetic biology. Biotechnol. Bioeng. 2016;113: 1777-1786. © 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
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois. .,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.
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69
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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71
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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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72
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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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73
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Li J, Lawton TJ, Kostecki JS, Nisthal A, Fang J, Mayo SL, Rosenzweig AC, Jewett MC. Cell‐free protein synthesis enables high yielding synthesis of an active multicopper oxidase. Biotechnol J 2015; 11:212-8. [DOI: 10.1002/biot.201500030] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/26/2015] [Accepted: 07/31/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Jian Li
- Department of 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
- Simpson Querrey Institute for BioNanotechnology in Medicine Northwestern University Chicago IL USA
| | - Thomas J. Lawton
- Department of Molecular Biosciences Northwestern University Evanston IL USA
| | - Jan S. Kostecki
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Alex Nisthal
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Jia Fang
- Department of Molecular Biosciences Northwestern University Evanston IL USA
| | - Stephen L. Mayo
- Division of Biological Sciences California Institute of Technology Pasadena CA USA
| | - Amy C. Rosenzweig
- Robert H. Lurie Comprehensive Cancer Center Northwestern University Chicago IL USA
- Department of Molecular Biosciences Northwestern University Evanston IL USA
- Department of Chemistry Northwestern University Evanston IL USA
| | - Michael C. Jewett
- Department of 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
- Simpson Querrey Institute for BioNanotechnology in Medicine Northwestern University Chicago IL USA
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74
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Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nat Commun 2015; 6:8168. [PMID: 26350765 PMCID: PMC4566161 DOI: 10.1038/ncomms9168] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/25/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the functional and structural consequences of site-specific protein phosphorylation has remained limited by our inability to produce phosphoproteins at high yields. Here we address this limitation by developing a cell-free protein synthesis (CFPS) platform that employs crude extracts from a genomically recoded strain of Escherichia coli for site-specific, co-translational incorporation of phosphoserine into proteins. We apply this system to the robust production of up to milligram quantities of human MEK1 kinase. Then, we recapitulate a physiological signalling cascade in vitro to evaluate the contributions of site-specific phosphorylation of mono- and doubly phosphorylated forms on MEK1 activity. We discover that only one phosphorylation event is necessary and sufficient for MEK1 activity. Our work sets the stage for using CFPS as a rapid high-throughput technology platform for direct expression of programmable phosphoproteins containing multiple phosphorylated residues. This work will facilitate study of phosphorylation-dependent structure–function relationships, kinase signalling networks and kinase inhibitor drugs. The inability to produce recombinant phosphoproteins has hindered research into their structure and function. Here the authors develop a cell-free protein synthesis platform to site-specifically incorporate phosphoserine into proteins at high yields, and recapitulate a MEK1 kinase signalling cascade.
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75
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Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 2015; 86:60-72. [DOI: 10.1016/j.ymeth.2015.05.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
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76
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77
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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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78
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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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79
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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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80
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Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
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Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
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Preparation of amino acid mixtures for cell-free expression systems. Biotechniques 2015; 58:40-3. [DOI: 10.2144/000114249] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/22/2014] [Indexed: 11/23/2022] Open
Abstract
Here we present a procedure for preparing amino acid mixtures–having both the desired composition and a physiological pH–at high concentrations for cell-free expression systems. Up to 2.1 mg/mL of active protein was synthesized in batch mode reactions with an all Escherichia coli cell-free expression system. Our method is fast, easy to execute, and economically advantageous compared to expensive commercial kits, making it useful for high-throughput experiments, incorporation of nonstandard amino acids, and cell-free metabolic engineering.
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Kelwick R, MacDonald JT, Webb AJ, Freemont P. Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol 2014; 2:60. [PMID: 25505788 PMCID: PMC4244866 DOI: 10.3389/fbioe.2014.00060] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 11/27/2022] Open
Abstract
Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.
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Affiliation(s)
- Richard Kelwick
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Alexander J Webb
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Paul Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
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83
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Soto CM. Protein engineering and other bio-synthetic routes for bio-based materials: current uses and potential applications. Front Chem 2014; 2:83. [PMID: 25353016 PMCID: PMC4195369 DOI: 10.3389/fchem.2014.00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/19/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carissa M Soto
- U. S. Naval Research Laboratory, Center for Bio/Molecular Science and Engineering Washington, DC, USA
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