1
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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2
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Multiple Gene Expression in Cell-Free Protein Synthesis Systems for Reconstructing Bacteriophages and Metabolic Pathways. Microorganisms 2022; 10:microorganisms10122477. [PMID: 36557730 PMCID: PMC9786908 DOI: 10.3390/microorganisms10122477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
As a fast and reliable technology with applications in diverse biological studies, cell-free protein synthesis has become popular in recent decades. The cell-free protein synthesis system can be considered a complex chemical reaction system that is also open to exogenous manipulation, including that which could otherwise potentially harm the cell's viability. On the other hand, since the technology depends on the cell lysates by which genetic information is transformed into active proteins, the whole system resembles the cell to some extent. These features make cell-free protein synthesis a valuable addition to synthetic biology technologies, expediting the design-build-test-learn cycle of synthetic biology routines. While the system has traditionally been used to synthesize one protein product from one gene addition, recent studies have employed multiple gene products in order to, for example, develop novel bacteriophages, viral particles, or synthetic metabolisms. Thus, we would like to review recent advancements in applying cell-free protein synthesis technology to synthetic biology, with an emphasis on multiple gene expressions.
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3
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Virosome, a promising delivery vehicle for siRNA delivery and its novel preparation method. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Ye Q, Lin X, Wang T, Cui Y, Jiang H, Lu Y. Programmable protein topology via
SpyCatcher‐SpyTag
chemistry in one‐pot cell‐free expression system. Protein Sci 2022; 31:e4335. [DOI: 10.1002/pro.4335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Qingning Ye
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
- College of New Energy and Materials China University of Petroleum Beijing China
| | - Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Yuntao Cui
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Hao Jiang
- School of Materials Science and Engineering Beijing Institute of Technology Beijing China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
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5
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A Crude Extract Preparation and Optimization from a Genomically Engineered Escherichia coli for the Cell-Free Protein Synthesis System: Practical Laboratory Guideline. Methods Protoc 2019; 2:mps2030068. [PMID: 31405077 PMCID: PMC6789667 DOI: 10.3390/mps2030068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/25/2023] Open
Abstract
With the advancement of synthetic biology, the cell-free protein synthesis (CFPS) system has been receiving the spotlight as a versatile toolkit for engineering natural and unnatural biological systems. The CFPS system reassembles the materials necessary for transcription and translation and recreates the in vitro protein synthesis environment by escaping a physical living boundary. The cell extract plays an essential role in this in vitro format. Here, we propose a practical protocol and method for Escherichia coli-derived cell extract preparation and optimization, which can be easily applied to both commercially available and genomically engineered E. coli strains. The protocol includes: (1) The preparation step for cell growth and harvest, (2) the thorough step-by-step procedures for E. coli cell extract preparation including the cell wash and lysis, centrifugation, runoff reaction, and dialysis, (3) the preparation for the CFPS reaction components and, (4) the quantification of cell extract and cell-free synthesized protein. We anticipate that the protocol in this research will provide a simple preparation and optimization procedure of a highly active E. coli cell extract.
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6
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Abstract
Cell-free systems (CFS) have recently evolved into key platforms for synthetic biology applications. Many synthetic biology tools have traditionally relied on cell-based systems, and while their adoption has shown great progress, the constraints inherent to the use of cellular hosts have limited their reach and scope. Cell-free systems, which can be thought of as programmable liquids, have removed many of these complexities and have brought about exciting opportunities for rational design and manipulation of biological systems. Here we review how these simple and accessible enzymatic systems are poised to accelerate the rate of advancement in synthetic biology and, more broadly, biotechnology.
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Affiliation(s)
- Aidan Tinafar
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada.
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7
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Yue K, Zhu Y, Kai L. Cell-Free Protein Synthesis: Chassis toward the Minimal Cell. Cells 2019; 8:cells8040315. [PMID: 30959805 PMCID: PMC6523147 DOI: 10.3390/cells8040315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
The quest for a minimal cell not only sheds light on the fundamental principles of life but also brings great advances in related applied fields such as general biotechnology. Minimal cell projects came from the study of a plausible route to the origin of life. Later on, research extended and also referred to the construction of artificial cells, or even more broadly, as in vitro synthetic biology. The cell-free protein synthesis (CFPS) techniques harness the central cellular activity of transcription/translation in an open environment, providing the framework for multiple cellular processes assembling. Therefore, CFPS systems have become the first choice in the construction of the minimal cell. In this review, we focus on the recent advances in the quantitative analysis of CFPS and on its advantage for addressing the bottom-up assembly of a minimal cell and illustrate the importance of systemic chassis behavior, such as stochasticity under a compartmentalized micro-environment.
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Affiliation(s)
- Ke Yue
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
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8
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Murphy TW, Sheng J, Naler LB, Feng X, Lu C. On-chip manufacturing of synthetic proteins for point-of-care therapeutics. MICROSYSTEMS & NANOENGINEERING 2019; 5:13. [PMID: 31057940 PMCID: PMC6431678 DOI: 10.1038/s41378-019-0051-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/29/2023]
Abstract
Therapeutic proteins have recently received increasing attention because of their clinical potential. Currently, most therapeutic proteins are produced on a large scale using various cell culture systems. However, storing and transporting these therapeutic proteins at low temperatures makes their distribution expensive and problematic, especially for applications in remote locations. To this end, an emerging solution is to use point-of-care technologies that enable immediate and accessible protein production at or near the patient's bedside. Here we present the development of "Therapeutics-On-a-Chip (TOC)", an integrated microfluidic platform that enables point-of-care synthesis and purification of therapeutic proteins. We used fresh and lyophilized materials for cell-free synthesis of therapeutic proteins on microfluidic chips and applied immunoprecipitation for highly efficient, on-chip protein purification. We first demonstrated this approach by expressing and purifying a reporter protein, green fluorescent protein. Next, we used TOC to produce cecropin B, an antimicrobial peptide that is widely used to control biofilm-associated diseases. We successfully synthesized and purified cecropin B at 63 ng/μl within 6 h with a 92% purity, followed by confirming its antimicrobial functionality using a growth inhibition assay. Our TOC technology provides a new platform for point-of-care production of therapeutic proteins at a clinically relevant quantity.
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Affiliation(s)
- Travis W. Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jiayuan Sheng
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Lynette B. Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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9
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10
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Process optimization for scalable E. coli extract preparation for cell-free protein synthesis. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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11
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Richardson D, Itkonen J, Nievas J, Urtti A, Casteleijn MG. Accelerated pharmaceutical protein development with integrated cell free expression, purification, and bioconjugation. Sci Rep 2018; 8:11967. [PMID: 30097621 PMCID: PMC6086869 DOI: 10.1038/s41598-018-30435-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 12/02/2022] Open
Abstract
The use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein’s stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split-intein mediated capture by use of capture peptides onto a solid surface was efficient at 89–93%. Proof-of-principle of light triggered release was compared to affinity chromatography (His6 fusion tag coupled with Ni-NTA). The latter was more efficient, but more time consuming. Light triggered release was clearly demonstrated. Moreover, we transferred biotin from the capture peptide to the target protein without further purification steps. Finally, the target protein was released in a buffer-volume and composition of our choice, omitting the need for protein concentration or changing the buffer. Split-intein mediated capture, protein trans splicing followed by light triggered release, and bioconjugation for proteins synthesized in cell free systems might be performed in an integrated workflow resulting in the fast production of the target protein.
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Affiliation(s)
- Dominique Richardson
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jaakko Itkonen
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Julia Nievas
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Arto Urtti
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Institute of Chemistry, St Petersburg State University, Petergoff, St Petersburg, Russian Federation
| | - Marco G Casteleijn
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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12
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Schörghuber J, Geist L, Platzer G, Feichtinger M, Bisaccia M, Scheibelberger L, Weber F, Konrat R, Lichtenecker RJ. Late metabolic precursors for selective aromatic residue labeling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:129-140. [PMID: 29808436 PMCID: PMC6096522 DOI: 10.1007/s10858-018-0188-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
In recent years, we developed a toolbox of heavy isotope containing compounds, which serve as metabolic amino acid precursors in the E. coli-based overexpression of aromatic residue labeled proteins. Our labeling techniques show excellent results both in terms of selectivity and isotope incorporation levels. They are additionally distinguished by low sample production costs and meet the economic demands to further implement protein NMR spectroscopy as a routinely used method in drug development processes. Different isotopologues allow for the assembly of optimized protein samples, which fulfill the requirements of various NMR experiments to elucidate protein structures, analyze conformational dynamics, or probe interaction surfaces. In the present article, we want to summarize the precursors we developed so far and give examples of their special value in the probing of protein-ligand interaction.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Michael Feichtinger
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Marilena Bisaccia
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Lukas Scheibelberger
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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13
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Hoffmann B, Löhr F, Laguerre A, Bernhard F, Dötsch V. Protein labeling strategies for liquid-state NMR spectroscopy using cell-free synthesis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 105:1-22. [PMID: 29548364 DOI: 10.1016/j.pnmrs.2017.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 05/17/2023]
Abstract
Preparation of a protein sample for liquid-state nuclear magnetic resonance (NMR) spectroscopy analysis requires optimization of many parameters. This review describes labeling strategies for obtaining assignments of protein resonances. Particular emphasis is placed on the advantages of cell-free protein production, which enables exclusive labeling of the protein of interest, thereby simplifying downstream processing steps and increasing the availability of different labeling strategies for a target protein. Furthermore, proteins can be synthesized in milligram yields, and the open nature of the cell-free system allows the addition of stabilizers, scrambling inhibitors or hydrophobic solubilization environments directly during the protein synthesis, which is especially beneficial for membrane proteins. Selective amino acid labeling of the protein of interest, the possibility of addressing scrambling issues and avoiding the need for labile amino acid precursors have been key factors in enabling the introduction of new assignment strategies based on different labeling schemes as well as on new pulse sequences. Combinatorial selective labeling methods have been developed to reduce the number of protein samples necessary to achieve a complete backbone assignment. Furthermore, selective labeling helps to decrease spectral overlap and overcome size limitations for solution NMR analysis of larger complexes, oligomers, intrinsically disordered proteins and membrane proteins.
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Affiliation(s)
- Beate Hoffmann
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
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14
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Didovyk A, Tonooka T, Tsimring L, Hasty J. Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression. ACS Synth Biol 2017; 6:2198-2208. [PMID: 28795570 DOI: 10.1021/acssynbio.7b00253] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducible, and a labor- and cost-effective approach for rapid production of bacterial lysates for cell-free gene expression. Using this method, robust and highly active bacterial cell lysates can be produced without specialized equipment at a wide range of scales, making cell-free gene expression easily and broadly accessible. Moreover, live autolysis strain can be freeze-dried directly and subsequently lysed upon rehydration to produce active lysate. We demonstrate the utility of autolysates for synthetic biology by regulating protein production and degradation, implementing quorum sensing, and showing quantitative protection of linear DNA templates by GamS protein. To allow versatile and sensitive β-galactosidase (LacZ) based readout we produce autolysates with no detectable background LacZ activity and use them to produce sensitive mercury(II) biosensors with LacZ-mediated colorimetric and fluorescent outputs. The autolysis approach can facilitate wider adoption of cell-free technology for cell-free gene expression as well as other synthetic biology and biotechnology applications, such as metabolic engineering, natural product biosynthesis, or proteomics.
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Affiliation(s)
- Andriy Didovyk
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Taishi Tonooka
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Lev Tsimring
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Jeff Hasty
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
- Department
of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Molecular
Biology Section, Division of Biological Science, University of California San Diego, La Jolla, California 92093, United States
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15
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Foshag D, Henrich E, Hiller E, Schäfer M, Kerger C, Burger-Kentischer A, Diaz-Moreno I, García-Mauriño SM, Dötsch V, Rupp S, Bernhard F. The E. coli S30 lysate proteome: A prototype for cell-free protein production. N Biotechnol 2017; 40:245-260. [PMID: 28943390 DOI: 10.1016/j.nbt.2017.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Protein production using processed cell lysates is a core technology in synthetic biology and these systems are excellent to produce difficult toxins or membrane proteins. However, the composition of the central lysate of cell-free systems is still a "black box". Escherichia coli lysates are most productive for cell-free expression, yielding several mgs of protein per ml of reaction. Their preparation implies proteome fractionation, resulting in strongly biased and yet unknown lysate compositions. Many metabolic pathways are expected to be truncated or completely removed. The lack of knowledge of basic cell-free lysate proteomes is a major bottleneck for directed lysate engineering approaches as well as for assay design using non-purified reaction mixtures. This study is starting to close this gap by providing a blueprint of the S30 lysate proteome derived from the commonly used E. coli strain A19. S30 lysates are frequently used for cell-free protein production and represent the basis of most commercial E. coli cell-free expression systems. A fraction of 821 proteins was identified as the core proteome in S30 lysates, representing approximately a quarter of the known E. coli proteome. Its classification into functional groups relevant for transcription/translation, folding, stability and metabolic processes will build the framework for tailored cell-free reactions. As an example, we show that SOS response induction during cultivation results in tuned S30 lysate with better folding capacity, and improved solubility and activity of synthesized proteins. The presented data and protocols can serve as a platform for the generation of customized cell-free systems and product analysis.
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Affiliation(s)
- Daniel Foshag
- Institute for Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Stuttgart, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ekkehard Hiller
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Miriam Schäfer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Christian Kerger
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | | | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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16
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Matthews CB, Wright C, Kuo A, Colant N, Westoby M, Love JC. Reexamining opportunities for therapeutic protein production in eukaryotic microorganisms. Biotechnol Bioeng 2017; 114:2432-2444. [DOI: 10.1002/bit.26378] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/19/2017] [Accepted: 07/03/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Catherine B. Matthews
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - Angel Kuo
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Noelle Colant
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - J. Christopher Love
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
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17
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Galán A, Comor L, Horvatić A, Kuleš J, Guillemin N, Mrljak V, Bhide M. Library-based display technologies: where do we stand? MOLECULAR BIOSYSTEMS 2017; 12:2342-58. [PMID: 27306919 DOI: 10.1039/c6mb00219f] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past two decades, library-based display technologies have been staggeringly optimized since their appearance in order to mimic the process of natural molecular evolution. Display technologies are essential for the isolation of specific high-affinity binding molecules (proteins, polypeptides, nucleic acids and others) for diagnostic and therapeutic applications in cancer, infectious diseases, autoimmune, neurodegenerative, inflammatory pathologies etc. Applications extend to other fields such as antibody and enzyme engineering, cell-free protein synthesis and the discovery of protein-protein interactions. Phage display technology is the most established of these methods but more recent fully in vitro alternatives, such as ribosome display, mRNA display, cis-activity based (CIS) display and covalent antibody display (CAD), as well as aptamer display and in vitro compartmentalization, offer advantages over phage in library size, speed and the display of unnatural amino acids and nucleotides. Altogether, they have produced several molecules currently approved or in diverse stages of clinical or preclinical testing and have provided researchers with tools to address some of the disadvantages of peptides and nucleotides such as their low affinity, low stability, high immunogenicity and difficulty to cross membranes. In this review we assess the fundamental technological features and point out some recent advances and applications of display technologies.
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Affiliation(s)
- Asier Galán
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Anita Horvatić
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair FP7, Internal diseases, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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18
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Sonnabend A, Spahn V, Stech M, Zemella A, Stein C, Kubick S. Production of G protein-coupled receptors in an insect-based cell-free system. Biotechnol Bioeng 2017; 114:2328-2338. [PMID: 28574582 PMCID: PMC5599999 DOI: 10.1002/bit.26346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 04/21/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
The biochemical analysis of human cell membrane proteins remains a challenging task due to the difficulties in producing sufficient quantities of functional protein. G protein‐coupled receptors (GPCRs) represent a main class of membrane proteins and drug targets, which are responsible for a huge number of signaling processes regulating various physiological functions in living cells. To circumvent the current bottlenecks in GPCR studies, we propose the synthesis of GPCRs in eukaryotic cell‐free systems based on extracts generated from insect (Sf21) cells. Insect cell lysates harbor the fully active translational and translocational machinery allowing posttranslational modifications, such as glycosylation and phosphorylation of de novo synthesized proteins. Here, we demonstrate the production of several GPCRs in a eukaryotic cell‐free system, performed within a short time and in a cost‐effective manner. We were able to synthesize a variety of GPCRs ranging from 40 to 133 kDa in an insect‐based cell‐free system. Moreover, we have chosen the μ opioid receptor (MOR) as a model protein to analyze the ligand binding affinities of cell‐free synthesized MOR in comparison to MOR expressed in a human cell line by “one‐point” radioligand binding experiments. Biotechnol. Bioeng. 2017;114: 2328–2338. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Viola Spahn
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Christoph Stein
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
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19
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Lu Y. Cell-free synthetic biology: Engineering in an open world. Synth Syst Biotechnol 2017; 2:23-27. [PMID: 29062958 PMCID: PMC5625795 DOI: 10.1016/j.synbio.2017.02.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/06/2017] [Indexed: 10/26/2022] Open
Abstract
Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.
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Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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20
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Sheng J, Lei S, Yuan L, Feng X. Cell-free protein synthesis of norovirus virus-like particles. RSC Adv 2017. [DOI: 10.1039/c7ra03742b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cell-free protein expression of norovirus virus-like-particles.
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Affiliation(s)
- Jiayuan Sheng
- Department of Biological Systems Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Shaohua Lei
- Department of Biomedical Sciences and Pathobiology
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
| | - Xueyang Feng
- Department of Biological Systems Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- USA
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21
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Ramaraju B, McFeeters H, Vogler B, McFeeters RL. Bacterial production of site specific 13C labeled phenylalanine and methodology for high level incorporation into bacterially expressed recombinant proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 67:23-34. [PMID: 28028744 PMCID: PMC5311020 DOI: 10.1007/s10858-016-0081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific 13C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles. Aromatic side chains have many of the same advantages as methyl containing amino acids including distinct 13C chemical shifts and multiple magnetically equivalent 1H positions. Herein we report economical bacterial production and one-step purification of phenylalanine with 13C incorporation at the Cα, Cγ and Cε positions, resulting in two isolated 1H-13C spin systems. We also present methodology to maximize incorporation of phenylalanine into recombinantly overexpressed proteins in bacteria and demonstrate compatibility with ILV-methyl labeling. Inexpensive, site specific isotope labeled phenylalanine adds another dimension to biomolecular NMR, opening new avenues of study.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Bernhard Vogler
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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22
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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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23
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Wronska MA, O'Connor IB, Tilbury MA, Srivastava A, Wall JG. Adding Functions to Biomaterial Surfaces through Protein Incorporation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5485-5508. [PMID: 27164952 DOI: 10.1002/adma.201504310] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 03/16/2016] [Indexed: 06/05/2023]
Abstract
The concept of biomaterials has evolved from one of inert mechanical supports with a long-term, biologically inactive role in the body into complex matrices that exhibit selective cell binding, promote proliferation and matrix production, and may ultimately become replaced by newly generated tissues in vivo. Functionalization of material surfaces with biomolecules is critical to their ability to evade immunorecognition, interact productively with surrounding tissues and extracellular matrix, and avoid bacterial colonization. Antibody molecules and their derived fragments are commonly immobilized on materials to mediate coating with specific cell types in fields such as stent endothelialization and drug delivery. The incorporation of growth factors into biomaterials has found application in promoting and accelerating bone formation in osteogenerative and related applications. Peptides and extracellular matrix proteins can impart biomolecule- and cell-specificities to materials while antimicrobial peptides have found roles in preventing biofilm formation on devices and implants. In this progress report, we detail developments in the use of diverse proteins and peptides to modify the surfaces of hard biomaterials in vivo and in vitro. Chemical approaches to immobilizing active biomolecules are presented, as well as platform technologies for isolation or generation of natural or synthetic molecules suitable for biomaterial functionalization.
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Affiliation(s)
- Małgorzata A Wronska
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Iain B O'Connor
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Maura A Tilbury
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - Akshay Srivastava
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
| | - J Gerard Wall
- Microbiology and Center for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Ireland
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24
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Georgi V, Georgi L, Blechert M, Bergmeister M, Zwanzig M, Wüstenhagen DA, Bier FF, Jung E, Kubick S. On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode. LAB ON A CHIP 2016; 16:269-81. [PMID: 26554896 DOI: 10.1039/c5lc00700c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Many pharmaceuticals are proteins or their development is based on proteins. Cell-free protein synthesis (CFPS) is an innovative alternative to conventional cell based systems which enables the production of proteins with complex and even new characteristics. However, the short lifetime, low protein production and expensive reagent costs are still limitations of CFPS. Novel automated microfluidic systems might allow continuous, controllable and resource conserving CFPS. The presented microfluidic TRITT platform (TRITT for Transcription - RNA Immobilization & Transfer - Translation) addresses the individual biochemical requirements of the transcription and the translation step of CFPS in separate compartments, and combines the reaction steps by quasi-continuous transfer of RNA templates to enable automated CFPS. In detail, specific RNA templates with 5' and 3' hairpin structures for stabilization against nucleases were immobilized during in vitro transcription by newly designed and optimized hybridization oligonucleotides coupled to magnetizable particles. Transcription compatibility and reusability for immobilization of these functionalized particles was successfully proven. mRNA transfer was realized on-chip by magnetic actuated particle transfer, RNA elution and fluid flow to the in vitro translation compartment. The applicability of the microfluidic TRITT platform for the production of the cytotoxic protein Pierisin with simultaneous incorporation of a non-canonical amino acid for fluorescence labeling was demonstrated. The new reaction mode (TRITT mode) is a modified linked mode that fulfills the precondition for an automated modular reactor system. By continual transfer of new mRNA, the novel procedure overcomes problems caused by nuclease digestion and hydrolysis of mRNA during TL in standard CFPS reactions.
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Affiliation(s)
- V Georgi
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany. and Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - L Georgi
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - M Blechert
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Bergmeister
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Zwanzig
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - D A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - F F Bier
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - E Jung
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - S Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
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25
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Joedicke L, Trenker R, Langer JD, Michel H, Preu J. Cell-free synthesis of isotopically labelled peptide ligands for the functional characterization of G protein-coupled receptors. FEBS Open Bio 2015; 6:90-102. [PMID: 27047736 PMCID: PMC4794788 DOI: 10.1002/2211-5463.12008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 11/24/2022] Open
Abstract
Cell‐free systems exploit the transcription and translation machinery of cells from different origins to produce proteins in a defined chemical environment. Due to its open nature, cell‐free protein production is a versatile tool to introduce specific labels such as heavy isotopes, non‐natural amino acids and tags into the protein while avoiding cell toxicity. In particular, radiolabelled peptides and proteins are valuable tools for the functional characterization of protein–protein interactions and for studying binding kinetics. In this study we evaluated cell‐free protein production for the generation of radiolabelled ligands for G protein‐coupled receptors (GPCRs). These receptors are seven‐transmembrane‐domain receptors activated by a plethora of extracellular stimuli including peptide ligands. Many GPCR peptide ligands contain disulphide bonds and are thus inherently difficult to produce in bacterial expression hosts or in Escherichia coli‐based cell‐free systems. Here, we established an adapted E. coli‐based cell‐free translation system for the production of disulphide bond‐containing GPCR peptide ligands and specifically introduce tritium labels for detection. The bacterial oxidoreductase DsbA is used as a chaperone to favour the formation of disulphide bonds and to enhance the yield of correctly folded proteins and peptides. We demonstrate the correct folding and formation of disulphide bonds and show high‐affinity ligand binding of the produced radio peptide ligands to the respective receptors. Thus, our system allows the fast, cost‐effective and reliable synthesis of custom GPCR peptide ligands for functional and structural studies.
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Affiliation(s)
- Lisa Joedicke
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Frankfurt am Main Germany
| | - Raphael Trenker
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Frankfurt am Main Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Frankfurt am Main Germany
| | - Julia Preu
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Frankfurt am Main Germany
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26
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Millet LJ, Lucheon JD, Standaert RF, Retterer ST, Doktycz MJ. Modular microfluidics for point-of-care protein purifications. LAB ON A CHIP 2015; 15:1799-811. [PMID: 25740172 DOI: 10.1039/c5lc00094g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. We demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.
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Affiliation(s)
- L J Millet
- Biological and Nanoscale Systems Group, Biosciences Division, Oak Ridge National Laboratory, PO Box 2008 MS 6445, Oak Ridge, TN 37831-6445, USA.
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27
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Andexer JN, Richter M. Emerging enzymes for ATP regeneration in biocatalytic processes. Chembiochem 2015; 16:380-6. [PMID: 25619338 DOI: 10.1002/cbic.201402550] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 12/15/2022]
Abstract
Adenosine-5'-triphosphate-dependent enzyme catalysed reactions are widespread in nature. Consequently, the enzymes involved have an intrinsic potential for use in syntheses of high value products. Although regeneration systems for ATP starting from adenosine-5'-diphosphate are available, certain limitations exist for both in vitro and in vivo applications requiring ATP regeneration from adenosine-5'-monophosphate, or adenosine. Following a short overview of the chemical and thermodynamic background, this Minireview focuses on emerging enzymes and methodologies for ATP regeneration. A large range of as yet unexploited reactions will be accessible with new, powerful, multistep ATP regeneration systems that use cheap phosphate donors and provide high longevity, compatibility, and robustness under process conditions. Their potential might go far beyond the direct use of ATP in enzymatic reactions; enzyme discovery, and engineering, as well as immobilisation strategies, will help to realise such systems.
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Affiliation(s)
- Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg (Germany).
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28
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Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. Drug Discov Today 2014; 19:1353-63. [PMID: 24980786 DOI: 10.1016/j.drudis.2014.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022]
Abstract
The Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando) uses similarity of compound-proteome interaction signatures to infer homology of compound/drug behavior. We constructed interaction signatures for 3733 human ingestible compounds covering 48,278 protein structures mapping to 2030 indications based on basic science methodologies to predict and analyze protein structure, function, and interactions developed by us and others. Our signature comparison and ranking approach yielded benchmarking accuracies of 12-25% for 1439 indications with at least two approved compounds. We prospectively validated 49/82 'high value' predictions from nine studies covering seven indications, with comparable or better activity to existing drugs, which serve as novel repurposed therapeutics. Our approach may be generalized to compounds beyond those approved by the FDA, and can also consider mutations in protein structures to enable personalization. Our platform provides a holistic multiscale modeling framework of complex atomic, molecular, and physiological systems with broader applications in medicine and engineering.
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Affiliation(s)
- Mark Minie
- University of Washington, Department of Bioengineering, Seattle, WA 98109, United States
| | - Gaurav Chopra
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States; University of California, San Francisco, Diabetes Center, San Francisco, CA 94143, United States
| | - Geetika Sethi
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States
| | - Jeremy Horst
- University of California, School of Medicine, San Francisco, CA 94143, United States
| | - George White
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States
| | - Ambrish Roy
- Georgia Institute of Technology, Center for the Study of Systems Biology, Atlanta, GA 30318, United States
| | - Kaushik Hatti
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, 560012, India
| | - Ram Samudrala
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States.
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29
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Smith MT, Wilding KM, Hunt JM, Bennett AM, Bundy BC. The emerging age of cell-free synthetic biology. FEBS Lett 2014; 588:2755-61. [PMID: 24931378 DOI: 10.1016/j.febslet.2014.05.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 01/16/2023]
Abstract
The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology.
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Affiliation(s)
- Mark Thomas Smith
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Kristen M Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Jeremy M Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Anthony M Bennett
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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30
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Harbers M. Wheat germ systems for cell-free protein expression. FEBS Lett 2014; 588:2762-73. [PMID: 24931374 DOI: 10.1016/j.febslet.2014.05.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.
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Affiliation(s)
- Matthias Harbers
- RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; CellFree Sciences Co., Ltd., 75-1, Ono-cho, Leading Venture Plaza 201, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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31
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Ebo DG, Van Vaerenbergh M, de Graaf DC, Bridts CH, De Clerck LS, Sabato V. In vitro diagnosis of Hymenoptera venom allergy and further development of component resolved diagnostics. Expert Rev Clin Immunol 2014; 10:375-84. [PMID: 24490811 DOI: 10.1586/1744666x.2014.881252] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For most people Hymenoptera stings result in transient and bothersome local inflammatory responses characterized by pain, itching, redness and swelling. In contrast, for those presenting an IgE-mediated allergic reaction, a re-sting may cause life-threatening reactions. In such patients, correct diagnosis is an absolute prerequisite for effective management, i.e. venom-specific immunotherapy. Generally, identification of the offending insect involves a detailed history along with quantification of venom-specific IgE antibodies and venom skin tests. Unfortunately, due to uncertainties associated with both tests, correct diagnosis is not always straightforward. This review summarizes the potentials and limitations of the various in vitro tests that are currently being used in the diagnosis of Hymenoptera venom allergy. Particular attention is paid to the potential of novel cellular tests such as basophil activation tests and component-resolved diagnosis with recombinant venom allergens in the diagnostic approach of patients with difficult diagnosis, i.e. cases in whom traditional venom specific IgE and skin tests yield equivocal or negative results. Finally, this review also covers the recent discoveries in the field of proteome research of Hymenoptera venoms and the selection of cell types for recombinant allergens production.
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Affiliation(s)
- Didier G Ebo
- Department of Immunology, Faculty of Medicine and Health Science, Allergology and Rheumatology, University Antwerp and Antwerp University Hospital, Antwerpen, Belgium
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Sheng J, Huang L, Zhu X, Cai J, Xu Z. Reconstitution of the peptidoglycan cytoplasmic precursor biosynthetic pathway in cell-free system and rapid screening of antisense oligonucleotides for Mur enzymes. Appl Microbiol Biotechnol 2014; 98:1785-94. [PMID: 24389752 DOI: 10.1007/s00253-013-5467-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
Bacterial peptidoglycan is the cell wall component responsible for various biological activities. Its cytoplasmic precursor UDP-N-acetylmuramyl pentapeptide is biosynthesized by the first six enzymes of peptidoglycan synthetic pathways (Mur enzymes), which are all proved to be important targets for antibiotic screening. In our present work, the genes encoding Mur enzymes from Escherichia coli were co-expressed in the cell-free protein synthesis (CFPS) system, and the activities of Mur enzymes derived from CFPS system were validated by the synthesis of the final product UDP-N-acetylmuramyl pentapeptide. Then this in vitro reconstituted Mur biosynthetic pathway was used to screen a panel of specific antisense oligonucleotides for MurA and MurB. The selected oligonucleotides were proved to eliminate the expression of Mur enzymes, and thus inhibit the Mur biosynthetic pathway. The present work not only developed a rapid method to reconstruct and regulate a biosynthetic pathway in vitro, but also may provide insight into the development of novel antibiotics targeting on peptidoglycan biosynthetic pathway.
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Affiliation(s)
- Jiayuan Sheng
- Department of Chemical and Biological Engineering, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, 310027, China
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Papaneophytou CP, Kontopidis G. Statistical approaches to maximize recombinant protein expression in Escherichia coli: a general review. Protein Expr Purif 2013; 94:22-32. [PMID: 24211770 DOI: 10.1016/j.pep.2013.10.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/16/2022]
Abstract
The supply of many valuable proteins that have potential clinical or industrial use is often limited by their low natural availability. With the modern advances in genomics, proteomics and bioinformatics, the number of proteins being produced using recombinant techniques is exponentially increasing and seems to guarantee an unlimited supply of recombinant proteins. The demand of recombinant proteins has increased as more applications in several fields become a commercial reality. Escherichia coli (E. coli) is the most widely used expression system for the production of recombinant proteins for structural and functional studies. However, producing soluble proteins in E. coli is still a major bottleneck for structural biology projects. One of the most challenging steps in any structural biology project is predicting which protein or protein fragment will express solubly and purify for crystallographic studies. The production of soluble and active proteins is influenced by several factors including expression host, fusion tag, induction temperature and time. Statistical designed experiments are gaining success in the production of recombinant protein because they provide information on variable interactions that escape the "one-factor-at-a-time" method. Here, we review the most important factors affecting the production of recombinant proteins in a soluble form. Moreover, we provide information about how the statistical design experiments can increase protein yield and purity as well as find conditions for crystal growth.
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Affiliation(s)
- Christos P Papaneophytou
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology - Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Technology Park of Thessaly, 1st Industrial Area, Volos 38500, Greece
| | - George Kontopidis
- Veterinary School, University of Thessaly, Trikalon 224, Karditsa 43100, Greece; Institute for Research and Technology - Thessaly (I.RE.TE.TH.), The Centre for Research & Technology Hellas (CE.R.TH.), Technology Park of Thessaly, 1st Industrial Area, Volos 38500, Greece.
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Cell-Free Systems: Functional Modules for Synthetic and Chemical Biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:67-102. [DOI: 10.1007/10_2013_185] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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