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Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. SMALL METHODS 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
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Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
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2
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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3
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Kelwick RJR, Webb AJ, Heliot A, Segura CT, Freemont PS. Opportunities to accelerate extracellular vesicle research with cell-free synthetic biology. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e90. [PMID: 38938277 PMCID: PMC11080881 DOI: 10.1002/jex2.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) are lipid-membrane nanoparticles that are shed or secreted by many different cell types. The EV research community has rapidly expanded in recent years and is leading efforts to deepen our understanding of EV biological functions in human physiology and pathology. These insights are also providing a foundation on which future EV-based diagnostics and therapeutics are poised to positively impact human health. However, current limitations in our understanding of EV heterogeneity, cargo loading mechanisms and the nascent development of EV metrology are all areas that have been identified as important scientific challenges. The field of synthetic biology is also contending with the challenge of understanding biological complexity as it seeks to combine multidisciplinary scientific knowledge with engineering principles, to build useful and robust biotechnologies in a responsible manner. Within this context, cell-free systems have emerged as a powerful suite of in vitro biotechnologies that can be employed to interrogate fundamental biological mechanisms, including the study of aspects of EV biogenesis, or to act as a platform technology for medical biosensors and therapeutic biomanufacturing. Cell-free gene expression (CFE) systems also enable in vitro protein production, including membrane proteins, and could conceivably be exploited to rationally engineer, or manufacture, EVs loaded with bespoke molecular cargoes for use in foundational or translational EV research. Our pilot data herein, also demonstrates the feasibility of cell-free EV engineering. In this perspective, we discuss the opportunities and challenges for accelerating EV research and healthcare applications with cell-free synthetic biology.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | - Alexander J. Webb
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | - Amelie Heliot
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | | | - Paul S. Freemont
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
- The London BiofoundryImperial College Translation & Innovation HubLondonUK
- UK Dementia Research Institute Care Research and Technology CentreImperial College London, Hammersmith CampusLondonUK
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4
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Haueis L, Stech M, Schneider E, Lanz T, Hebel N, Zemella A, Kubick S. Rapid One-Step Capturing of Native, Cell-Free Synthesized and Membrane-Embedded GLP-1R. Int J Mol Sci 2023; 24:ijms24032808. [PMID: 36769142 PMCID: PMC9917595 DOI: 10.3390/ijms24032808] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are of outstanding pharmacological interest as they are abundant in cell membranes where they perform diverse functions that are closely related to the vitality of cells. The analysis of GPCRs in natural membranes is laborious, as established methods are almost exclusively cell culture-based and only a few methods for immobilization in a natural membrane outside the cell are known. Within this study, we present a one-step, fast and robust immobilization strategy of the GPCR glucagon-like peptide 1 receptor (GLP-1R). GLP-1R was synthesized in eukaryotic lysates harboring endogenous endoplasmic reticulum-derived microsomes enabling the embedment of GLP-1R in a natural membrane. Interestingly, we found that these microsomes spontaneously adsorbed to magnetic Neutravidin beads thus providing immobilized membrane protein preparations which required no additional manipulation of the target receptor or its supporting membrane. The accessibility of the extracellular domain of membrane-embedded and bead-immobilized GLP-1R was demonstrated by bead-based enzyme-linked immunosorbent assay (ELISA) using GLP-1R-specific monoclonal antibodies. In addition, ligand binding of immobilized GLP-1R was verified in a radioligand binding assay. In summary, we present an easy and straightforward synthesis and immobilization methodology of an active GPCR which can be beneficial for studying membrane proteins in general.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Correspondence:
| | | | - Thorsten Lanz
- 3B Pharmaceuticals GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Nicole Hebel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- 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
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
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5
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Walter RM, Zemella A, Schramm M, Kiebist J, Kubick S. Vesicle-based cell-free synthesis of short and long unspecific peroxygenases. Front Bioeng Biotechnol 2022; 10:964396. [PMID: 36394036 PMCID: PMC9663805 DOI: 10.3389/fbioe.2022.964396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal enzymes that catalyze the oxyfunctionalization of non-activated hydrocarbons, making them valuable biocatalysts. Despite the increasing interest in UPOs that has led to the identification of thousands of putative UPO genes, only a few of these have been successfully expressed and characterized. There is currently no universal expression system in place to explore their full potential. Cell-free protein synthesis has proven to be a sophisticated technique for the synthesis of difficult-to-express proteins. In this work, we aimed to establish an insect-based cell-free protein synthesis (CFPS) platform to produce UPOs. CFPS relies on translationally active cell lysates rather than living cells. The system parameters can thus be directly manipulated without having to account for cell viability, thereby making it highly adaptable. The insect-based lysate contains translocationally active, ER-derived vesicles, called microsomes. These microsomes have been shown to allow efficient translocation of proteins into their lumen, promoting post-translational modifications such as disulfide bridge formation and N-glycosylations. In this study the ability of a redox optimized, vesicle-based, eukaryotic CFPS system to synthesize functional UPOs was explored. The influence of different reaction parameters as well as the influence of translocation on enzyme activity was evaluated for a short UPO from Marasmius rotula and a long UPO from Agrocybe aegerita. The capability of the CFPS system described here was demonstrated by the successful synthesis of a novel UPO from Podospora anserina, thus qualifying CFPS as a promising tool for the identification and evaluation of novel UPOs and variants thereof.
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Affiliation(s)
- Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Marina Schramm
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jan Kiebist
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry – Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus – Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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6
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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7
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Hershewe JM, Warfel KF, Iyer SM, Peruzzi JA, Sullivan CJ, Roth EW, DeLisa MP, Kamat NP, Jewett MC. Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles. Nat Commun 2021; 12:2363. [PMID: 33888690 PMCID: PMC8062659 DOI: 10.1038/s41467-021-22329-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Cell-free gene expression (CFE) systems from crude cellular extracts have attracted much attention for biomanufacturing and synthetic biology. However, activating membrane-dependent functionality of cell-derived vesicles in bacterial CFE systems has been limited. Here, we address this limitation by characterizing native membrane vesicles in Escherichia coli-based CFE extracts and describing methods to enrich vesicles with heterologous, membrane-bound machinery. As a model, we focus on bacterial glycoengineering. We first use multiple, orthogonal techniques to characterize vesicles and show how extract processing methods can be used to increase concentrations of membrane vesicles in CFE systems. Then, we show that extracts enriched in vesicle number also display enhanced concentrations of heterologous membrane protein cargo. Finally, we apply our methods to enrich membrane-bound oligosaccharyltransferases and lipid-linked oligosaccharides for improving cell-free N-linked and O-linked glycoprotein synthesis. We anticipate that these methods will facilitate on-demand glycoprotein production and enable new CFE systems with membrane-associated activities.
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Affiliation(s)
- Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Shaelyn M Iyer
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Claretta J Sullivan
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization and Experimentation (NUANCE) Center, Tech Institute A/B Wing A173, Evanston, IL, 60208, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
- Biomedical and Biological Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Neha P Kamat
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Technological Institute E310, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
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8
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Batista AC, Soudier P, Kushwaha M, Faulon J. Optimising protein synthesis in cell‐free systems, a review. ENGINEERING BIOLOGY 2021; 5:10-19. [PMID: 36968650 PMCID: PMC9996726 DOI: 10.1049/enb2.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.
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Affiliation(s)
- Angelo C. Batista
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Paul Soudier
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Manish Kushwaha
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Jean‐Loup Faulon
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
- SYNBIOCHEM Center School of Chemistry Manchester Institute of Biotechnology The University of Manchester Manchester UK
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9
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Abarghooi Kahaki F, Monzavi S, Bamehr H, Bandani E, Payandeh Z, Jahangiri A, Khalili S. Expression and Purification of Membrane Proteins in Different Hosts. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-10009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Hershewe J, Kightlinger W, Jewett MC. Cell-free systems for accelerating glycoprotein expression and biomanufacturing. J Ind Microbiol Biotechnol 2020; 47:977-991. [PMID: 33090335 PMCID: PMC7578589 DOI: 10.1007/s10295-020-02321-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/03/2020] [Indexed: 12/17/2022]
Abstract
Protein glycosylation, the enzymatic modification of amino acid sidechains with sugar moieties, plays critical roles in cellular function, human health, and biotechnology. However, studying and producing defined glycoproteins remains challenging. Cell-free glycoprotein synthesis systems, in which protein synthesis and glycosylation are performed in crude cell extracts, offer new approaches to address these challenges. Here, we review versatile, state-of-the-art systems for biomanufacturing glycoproteins in prokaryotic and eukaryotic cell-free systems with natural and synthetic N-linked glycosylation pathways. We discuss existing challenges and future opportunities in the use of cell-free systems for the design, manufacture, and study of glycoprotein biomedicines.
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Affiliation(s)
- Jasmine Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA. .,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North Saint Clair Street, Suite 1200, Chicago, IL, 60611-3068, USA. .,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL, 60611-2875, USA.
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11
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Abstract
Proteins are the main source of drug targets and some of them possess therapeutic potential themselves. Among them, membrane proteins constitute approximately 50% of the major drug targets. In the drug discovery pipeline, rapid methods for producing different classes of proteins in a simple manner with high quality are important for structural and functional analysis. Cell-free systems are emerging as an attractive alternative for the production of proteins due to their flexible nature without any cell membrane constraints. In a bioproduction context, open systems based on cell lysates derived from different sources, and with batch-to-batch consistency, have acted as a catalyst for cell-free synthesis of target proteins. Most importantly, proteins can be processed for downstream applications like purification and functional analysis without the necessity of transfection, selection, and expansion of clones. In the last 5 years, there has been an increased availability of new cell-free lysates derived from multiple organisms, and their use for the synthesis of a diverse range of proteins. Despite this progress, major challenges still exist in terms of scalability, cost effectiveness, protein folding, and functionality. In this review, we present an overview of different cell-free systems derived from diverse sources and their application in the production of a wide spectrum of proteins. Further, this article discusses some recent progress in cell-free systems derived from Chinese hamster ovary and Sf21 lysates containing endogenous translocationally active microsomes for the synthesis of membrane proteins. We particularly highlight the usage of internal ribosomal entry site sequences for more efficient protein production, and also the significance of site-specific incorporation of non-canonical amino acids for labeling applications and creation of antibody drug conjugates using cell-free systems. We also discuss strategies to overcome the major challenges involved in commercializing cell-free platforms from a laboratory level for future drug development.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- 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.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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12
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Thoring L, Zemella A, Wüstenhagen D, Kubick S. Accelerating the Production of Druggable Targets: Eukaryotic Cell-Free Systems Come into Focus. Methods Protoc 2019; 2:mps2020030. [PMID: 31164610 PMCID: PMC6632147 DOI: 10.3390/mps2020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/05/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
In the biopharmaceutical pipeline, protein expression systems are of high importance not only for the production of biotherapeutics but also for the discovery of novel drugs. The vast majority of drug targets are proteins, which need to be characterized and validated prior to the screening of potential hit components and molecules. A broad range of protein expression systems is currently available, mostly based on cellular organisms of prokaryotic and eukaryotic origin. Prokaryotic cell-free systems are often the system of choice for drug target protein production due to the simple generation of expression hosts and low cost of preparation. Limitations in the production of complex mammalian proteins appear due to inefficient protein folding and posttranslational modifications. Alternative protein production systems, so-called eukaryotic cell-free protein synthesis systems based on eukaryotic cell-lysates, close the gap between a fast protein generation system and a high quality of complex mammalian proteins. In this study, we show the production of druggable target proteins in eukaryotic cell-free systems. Functional characterization studies demonstrate the bioactivity of the proteins and underline the potential for eukaryotic cell-free systems to significantly improve drug development pipelines.
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Affiliation(s)
- Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany.
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany.
| | - Doreen Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany.
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany.
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13
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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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14
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Nevenzal H, Noach-Hirsh M, Skornik-Bustan O, Brio L, Barbiro-Michaely E, Glick Y, Avrahami D, Lahmi R, Tzur A, Gerber D. A high-throughput integrated microfluidics method enables tyrosine autophosphorylation discovery. Commun Biol 2019; 2:42. [PMID: 30729180 PMCID: PMC6353932 DOI: 10.1038/s42003-019-0286-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 12/21/2018] [Indexed: 01/22/2023] Open
Abstract
Autophosphorylation of receptor and non-receptor tyrosine kinases is a common molecular switch with broad implications for pathogeneses and therapy of cancer and other human diseases. Technologies for large-scale discovery and analysis of autophosphorylation are limited by the inherent difficulty to distinguish between phosphorylation and autophosphorylation in vivo and by the complexity associated with functional assays of receptors kinases in vitro. Here, we report a method for the direct detection and analysis of tyrosine autophosphorylation using integrated microfluidics and freshly synthesized protein arrays. We demonstrate the efficacy of our platform in detecting autophosphorylation activity of soluble and transmembrane tyrosine kinases, and the dependency of in vitro autophosphorylation assays on membranes. Our method, Integrated Microfluidics for Autophosphorylation Discovery (IMAD), is high-throughput, requires low reaction volumes and can be applied in basic and translational research settings. To our knowledge, it is the first demonstration of posttranslational modification analysis of membrane protein arrays.
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Affiliation(s)
- Hadas Nevenzal
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Meirav Noach-Hirsh
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Or Skornik-Bustan
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Lev Brio
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Efrat Barbiro-Michaely
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Yair Glick
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Dorit Avrahami
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Roxane Lahmi
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Amit Tzur
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Building #206, Ramat-Gan, 5290002 Israel
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15
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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Wege zur Synthese einer Zelle aus nicht lebenden Komponenten. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802288] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Petra Schwille
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Joachim Spatz
- MPI für medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | | | - Eberhard Bodenschatz
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Stephan Herminghaus
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Victor Sourjik
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Tobias J. Erb
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Philippe Bastiaens
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Reinhard Lipowsky
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Anthony Hyman
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Peter Dabrock
- Friedrich-Alexander-Universität Erlangen-Nürnberg; Fachbereich Theologie; Kochstraße 6 91054 Erlangen Deutschland
| | - Jean-Christophe Baret
- University of Bordeaux - Centre de Recherches Paul Pascal; 115 Avenue Schweitze 33600 Pessac Frankreich
| | - Tanja Vidakovic-Koch
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
| | - Peter Bieling
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Rumiana Dimova
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Hannes Mutschler
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Tom Robinson
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - T.-Y. Dora Tang
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Seraphine Wegner
- MPI für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kai Sundmacher
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
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17
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Avenues Towards Creating Cells from the Bottom Up. Angew Chem Int Ed Engl 2018; 57:13382-13392. [PMID: 29749673 DOI: 10.1002/anie.201802288] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/03/2018] [Indexed: 12/18/2022]
Abstract
A large German research consortium mainly within the Max Planck Society ("MaxSynBio") was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom-up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non-living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.
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Affiliation(s)
- Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Joachim Spatz
- MPI for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - Eberhard Bodenschatz
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Stephan Herminghaus
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Victor Sourjik
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Tobias J Erb
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Philippe Bastiaens
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Reinhard Lipowsky
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Anthony Hyman
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Peter Dabrock
- Friedrich-Alexander University Erlangen-Nuremberg, Department of Theology, Kochstraße 6, 91054, Erlangen, Germany
| | - Jean-Christophe Baret
- University of Bordeaux -Centre de Recherches Paul Pascal, 115 Avenue Schweitze, 33600, Pessac, France
| | - Tanja Vidakovic-Koch
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Peter Bieling
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Rumiana Dimova
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Hannes Mutschler
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tom Robinson
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - T-Y Dora Tang
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Seraphine Wegner
- MPI for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kai Sundmacher
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
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18
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Abstract
Cell-free production is a valuable and alternative method for the synthesis of membrane proteins. This system offers openness allowing the researchers to modify the reaction conditions without any boundaries. Additionally, the cell-free reactions are scalable from 20 μL up to several mL, faster and suitable for the high-throughput protein production. Here, we present two cell-free systems derived from Escherichia coli (E. coli) and Spodoptera frugiperda (Sf21) lysates. In the case of the E. coli cell-free system, nanodiscs are used for the solubilization and purification of membrane proteins. In the case of the Sf21 system, endogenous microsomes with an active translocon complex are present within the lysates which facilitate the incorporation of the bacterial potassium channel KcsA within the microsomal membranes. Following cell-free synthesis, these microsomes are directly used for the functional analysis of membrane proteins.
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19
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Zemella A, Thoring L, Hoffmeister C, Šamalíková M, Ehren P, Wüstenhagen DA, Kubick S. Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin. Sci Rep 2018; 8:8514. [PMID: 29867209 PMCID: PMC5986796 DOI: 10.1038/s41598-018-26936-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
As one of the most complex post-translational modification, glycosylation is widely involved in cell adhesion, cell proliferation and immune response. Nevertheless glycoproteins with an identical polypeptide backbone mostly differ in their glycosylation patterns. Due to this heterogeneity, the mapping of different glycosylation patterns to their associated function is nearly impossible. In the last years, glycoengineering tools including cell line engineering, chemoenzymatic remodeling and site-specific glycosylation have attracted increasing interest. The therapeutic hormone erythropoietin (EPO) has been investigated in particular by various groups to establish a production process resulting in a defined glycosylation pattern. However commercially available recombinant human EPO shows batch-to-batch variations in its glycoforms. Therefore we present an alternative method for the synthesis of active glycosylated EPO with an engineered O-glycosylation site by combining eukaryotic cell-free protein synthesis and site-directed incorporation of non-canonical amino acids with subsequent chemoselective modifications.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany
| | - Mária Šamalíková
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany
| | - Patricia Ehren
- University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam, 14476, Germany.
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20
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Schoborg JA, Jewett MC. Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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
| | - 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
- 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
- Center for Synthetic Biology; Northwestern University, 2145 Sheridan Road; Evanston IL 60208-3120 USA
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21
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Abstract
Tyrosine phosphorylation is an essential posttranslational modification in intracellular signaling molecules. Since tyrosine phosphorylation occurs in less than 0.1 % of all phosphorylated amino acids in mammalian cells, it is difficult to detect the nascent phosphotyrosine at a high signal-to-noise ratio due to high intracellular backgrounds (i.e., unexpected crosstalks among endogenous signaling molecules). In order to address this issue, we reconstituted the mammalian signaling pathway involving an extracellular ligand and a receptor tyrosine kinase (RTK) in Saccharomyces cerevisiae, a lower eukaryote that lacks endogenous tyrosine kinases. In this chapter, we describe a method for high-throughput analysis of ligand-receptor interaction by combining the yeast cell-surface display technique with an automated single-cell analysis and isolation system. Yeast cells coexpressing the cell-wall-anchored form of the human epidermal growth factor (EGF) and the human EGF receptor (EGFR) fused with a signal peptide at the N terminus facilitated the interaction of EGF with EGFR in an autocrine manner, followed by EGFR oligomerization and subsequent autophosphorylation. Furthermore, yeast cells expressing cell-wall-anchored forms of a conformationally constrained random peptide library instead of EGF are treated with a fluorophore-labeled anti-phosphorylated EGFR antibody and then subjected to the automated single-cell analysis and isolation system. The yeast cells with the highest level of fluorescence were shown to display novel and efficient EGFR agonistic peptides. Thus, our yeast display technique serves as a quantitative measurement for RTK activation, which is applicable to high-throughput de novo screening of RTK agonistic peptides.
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22
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Schoborg JA, Hershewe JM, Stark JC, Kightlinger W, Kath JE, Jaroentomeechai T, Natarajan A, DeLisa MP, Jewett MC. A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases. Biotechnol Bioeng 2017; 115:739-750. [PMID: 29178580 DOI: 10.1002/bit.26502] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/17/2022]
Abstract
Protein glycosylation, or the attachment of sugar moieties (glycans) to proteins, is important for protein stability, activity, and immunogenicity. However, understanding the roles and regulations of site-specific glycosylation events remains a significant challenge due to several technological limitations. These limitations include a lack of available tools for biochemical characterization of enzymes involved in glycosylation. A particular challenge is the synthesis of oligosaccharyltransferases (OSTs), which catalyze the attachment of glycans to specific amino acid residues in target proteins. The difficulty arises from the fact that canonical OSTs are large (>70 kDa) and possess multiple transmembrane helices, making them difficult to overexpress in living cells. Here, we address this challenge by establishing a bacterial cell-free protein synthesis platform that enables rapid production of a variety of OSTs in their active conformations. Specifically, by using lipid nanodiscs as cellular membrane mimics, we obtained yields of up to 420 μg/ml for the single-subunit OST enzyme, "Protein glycosylation B" (PglB) from Campylobacter jejuni, as well as for three additional PglB homologs from Campylobacter coli, Campylobacter lari, and Desulfovibrio gigas. Importantly, all of these enzymes catalyzed N-glycosylation reactions in vitro with no purification or processing needed. Furthermore, we demonstrate the ability of cell-free synthesized OSTs to glycosylate multiple target proteins with varying N-glycosylation acceptor sequons. We anticipate that this broadly applicable production method will advance glycoengineering efforts by enabling preparative expression of membrane-embedded OSTs from all kingdoms of life.
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Affiliation(s)
- Jennifer A Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois.,Master of Biotechnology Program, Northwestern University, Evanston, Illinois
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - James E Kath
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois
| | - Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York
| | | | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York.,Department of Microbiology, Cornell University, Ithaca, New York
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Evanston, Illinois.,Master of Biotechnology Program, Northwestern University, Evanston, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois
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23
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Dondapati SK, Wüstenhagen DA, Strauch E, Kubick S. Cell-free production of pore forming toxins: Functional analysis of thermostable direct hemolysin from Vibrio parahaemolyticus. Eng Life Sci 2017; 18:140-148. [PMID: 29497355 PMCID: PMC5814925 DOI: 10.1002/elsc.201600259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 09/19/2017] [Accepted: 11/02/2017] [Indexed: 01/21/2023] Open
Abstract
The pore forming characteristic of TDH1 and TDH2 variants of thermostable direct hemolysin (TDH), a major toxin involved in the pathogenesis of Vibrio parahaemolyticus, was studied on a planar lipid bilayer painted over individual picoliter cavities containing microelectrodes assembled in a multiarray. Both proteins formed pores upon insertion into the lipid bilayer which was shown as a shift in the conductance from the baseline current. TDH2 protein was able to produce stable currents and the currents were influenced by external factors like concentration, type of salt and voltage. The pore currents were influenced and showed a detectable response in the presence of polymers which makes them suitable for biotechnology applications.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Eckhard Strauch
- Federal Institute for Risk Assessment Department of Biological Safety National Reference Laboratory for Monitoring Bacteriological Contamination of Bivalve Molluscs Berlin Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
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24
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25
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Jérôme V, Thoring L, Salzig D, Kubick S, Freitag R. Comparison of cell-based versus cell-free mammalian systems for the production of a recombinant human bone morphogenic growth factor. Eng Life Sci 2017; 17:1097-1107. [PMID: 32624737 DOI: 10.1002/elsc.201700005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/14/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022] Open
Abstract
The human bone morphogenetic protein-2 (hBMP2) is a glycoprotein, which induces de novo bone formation. Here, recombinant production in stably transfected Chinese Hamster Ovary (CHO) cells is compared to transient expression in Human Embryo Kidney (HEK) cells and cell-free synthesis in CHO cell lysates containing microsomal structures as sites of post-translational processing. In case of the stably transfected cells, growth rates and viabilities were similar to those of the parent cells, while entry into the death phase of the culture was delayed. The maximum achievable rhBMP2 concentration in these cultures was 153 pg/mL. Up to 280 ng/mL could be produced in the transient expression system. In both cases the rhBMP-2 was found to interact with the producer cells, which presumably contributed to the low yields. In the cell-free system, hBMP2 yields could be increased to almost 40 μg/mL, reached within three hours. The cell-free system thus approached productivities for the active (renatured) protein previously only recorded for bacterial hosts, while assuring comprehensive post-translational processing.
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Affiliation(s)
- Valérie Jérôme
- Chair for Process Biotechnology University of Bayreuth Germany
| | - Lena Thoring
- Department of Cell-free and Cell-based Bioproduction, Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Germany
| | - Denise Salzig
- Chair for Process Biotechnology University of Bayreuth Germany
| | - Stefan Kubick
- Department of Cell-free and Cell-based Bioproduction, Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Germany
| | - Ruth Freitag
- Chair for Process Biotechnology University of Bayreuth Germany
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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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Quast RB, Sonnabend A, Stech M, Wüstenhagen DA, Kubick S. High-yield cell-free synthesis of human EGFR by IRES-mediated protein translation in a continuous exchange cell-free reaction format. Sci Rep 2016; 6:30399. [PMID: 27456041 PMCID: PMC4960648 DOI: 10.1038/srep30399] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 07/01/2016] [Indexed: 01/18/2023] Open
Abstract
Cell-free protein synthesis systems derived from eukaryotic sources often provide comparatively low amounts of several μg per ml of de novo synthesized membrane protein. In order to overcome this, we herein demonstrate the high-yield cell-free synthesis of the human EGFR in a microsome-containing system derived from cultured Sf21 cells. Yields were increased more than 100-fold to more than 285 μg/ml by combination of IRES-mediated protein translation with a continuous exchange cell-free reaction format that allowed for prolonged reaction lifetimes exceeding 24 hours. In addition, an orthogonal cell-free translation system is presented that enabled the site-directed incorporation of p-Azido-L-phenylalanine by amber suppression. Functionality of cell-free synthesized receptor molecules is demonstrated by investigation of autophosphorylation activity in the absence of ligand and interaction with the cell-free synthesized adapter molecule Grb2.
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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, D-14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476 Potsdam, Germany
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Mohr BP, Retterer ST, Doktycz MJ. While-you-wait proteins? Producing biomolecules at the point of need. Expert Rev Proteomics 2016; 13:707-9. [PMID: 27402489 DOI: 10.1080/14789450.2016.1209415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Benjamin P Mohr
- a Bredesen Center for Interdisciplinary Research , University of Tennessee , Knoxville , TN , USA.,b Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , TN , USA
| | - Scott T Retterer
- a Bredesen Center for Interdisciplinary Research , University of Tennessee , Knoxville , TN , USA.,b Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , TN , USA.,c Center for Nanophase and Material Sciences , Oak Ridge National Laboratory , Oak Ridge , TN , USA
| | - Mitchel J Doktycz
- a Bredesen Center for Interdisciplinary Research , University of Tennessee , Knoxville , TN , USA.,b Biosciences Division , Oak Ridge National Laboratory , Oak Ridge , TN , USA.,c Center for Nanophase and Material Sciences , Oak Ridge National Laboratory , Oak Ridge , TN , USA
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Körfer G, Pitzler C, Vojcic L, Martinez R, Schwaneberg U. In vitro flow cytometry-based screening platform for cellulase engineering. Sci Rep 2016; 6:26128. [PMID: 27184298 PMCID: PMC4869107 DOI: 10.1038/srep26128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Ultrahigh throughput screening (uHTS) plays an essential role in directed evolution for tailoring biocatalysts for industrial applications. Flow cytometry-based uHTS provides an efficient coverage of the generated protein sequence space by analysis of up to 107 events per hour. Cell-free enzyme production overcomes the challenge of diversity loss during the transformation of mutant libraries into expression hosts, enables directed evolution of toxic enzymes, and holds the promise to efficiently design enzymes of human or animal origin. The developed uHTS cell-free compartmentalization platform (InVitroFlow) is the first report in which a flow cytometry-based screened system has been combined with compartmentalized cell-free expression for directed cellulase enzyme evolution. InVitroFlow was validated by screening of a random cellulase mutant library employing a novel screening system (based on the substrate fluorescein-di-β-D-cellobioside), and yielded significantly improved cellulase variants (e.g. CelA2-H288F-M1 (N273D/H288F/N468S) with 13.3-fold increased specific activity (220.60 U/mg) compared to CelA2 wildtype: 16.57 U/mg).
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Affiliation(s)
| | | | - Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.,DWI an der RWTH Aachen e.V, Forckenbeckstraße 50, 52056 Aachen, Germany
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Pathogen receptor discovery with a microfluidic human membrane protein array. Proc Natl Acad Sci U S A 2016; 113:4344-9. [PMID: 27044079 DOI: 10.1073/pnas.1518698113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The discovery of how a pathogen invades a cell requires one to determine which host cell receptors are exploited. This determination is a challenging problem because the receptor is invariably a membrane protein, which represents an Achilles heel in proteomics. We have developed a universal platform for high-throughput expression and interaction studies of membrane proteins by creating a microfluidic-based comprehensive human membrane protein array (MPA). The MPA is, to our knowledge, the first of its kind and offers a powerful alternative to conventional proteomics by enabling the simultaneous study of 2,100 membrane proteins. We characterized direct interactions of a whole nonenveloped virus (simian virus 40), as well as those of the hepatitis delta enveloped virus large form antigen, with candidate host receptors expressed on the MPA. Selected newly discovered membrane protein-pathogen interactions were validated by conventional methods, demonstrating that the MPA is an important tool for cellular receptor discovery and for understanding pathogen tropism.
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Yoshimoto N, Ikeda Y, Tatematsu K, Iijima M, Nakai T, Okajima T, Tanizawa K, Kuroda S. Cytokine-dependent activation of JAK-STAT pathway in Saccharomyces cerevisiae. Biotechnol Bioeng 2016; 113:1796-804. [PMID: 26853220 DOI: 10.1002/bit.25948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/28/2015] [Accepted: 02/03/2016] [Indexed: 01/28/2023]
Abstract
Protein phosphorylation is an important post-translational modification for intracellular signaling molecules, mostly found in serine and threonine residues. Tyrosine phosphorylations are very few events (less than 0.1% to phosphorylated serine/threonine residues), but capable of governing cell fate decisions involved in proliferation, differentiation, apoptosis, and oncogenic transformation. Hence, it is important for drug discovery and system biology to measure the intracellular level of phosphotyrosine. Although mammalian cells have been conventionally utilized for this purpose, accurate determination of phosphotyrosine level often suffers from high background due to the unexpected crosstalk among endogenous signaling molecules. This situation led us firstly to establish the ligand-induced activation of homomeric receptor tyrosine kinase (i.e., epidermal growth factor receptor) in Saccharomyces cerevisiae, a lower eukaryote possessing organelles similar to higher eukaryote but not showing substantial level of tyrosine kinase activity. In this study, we expressed heteromeric receptor tyrosine kinase (i.e., a complex of interleukin-5 receptor (IL5R) α chain, common β chain, and JAK2 tyrosine kinase) in yeast. When coexpressed with a cell wall-anchored form of IL5, the yeast exerted the autophosphorylation of JAK2, followed by the phosphorylation of transcription factor STAT5a and subsequent nuclear accumulation of phosphorylated STAT5a. Taken together, yeast could be an ideal host for sensitive detection of phosphotyrosine generated by a wide variety of tyrosine kinases. Biotechnol. Bioeng. 2016;113: 1796-1804. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nobuo Yoshimoto
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yuko Ikeda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Kenji Tatematsu
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Masumi Iijima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Tadashi Nakai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Toshihide Okajima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Katsuyuki Tanizawa
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
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32
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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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Salehi ASM, Smith MT, Bennett AM, Williams JB, Pitt WG, Bundy BC. Cell‐free protein synthesis of a cytotoxic cancer therapeutic: Onconase production and a just‐add‐water cell‐free system. Biotechnol J 2015; 11:274-81. [DOI: 10.1002/biot.201500237] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/30/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Amin S. M. Salehi
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Mark Thomas Smith
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Anthony M. Bennett
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Jacob B. Williams
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - William G. Pitt
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Bradley C. Bundy
- Department of Chemical Engineering Brigham Young University Provo Utah USA
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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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35
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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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36
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Quast RB, Kortt O, Henkel J, Dondapati SK, Wüstenhagen DA, Stech M, Kubick S. Automated production of functional membrane proteins using eukaryotic cell-free translation systems. J Biotechnol 2015; 203:45-53. [PMID: 25828454 DOI: 10.1016/j.jbiotec.2015.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 12/14/2022]
Abstract
Due to their high abundance and pharmacological relevance there is a growing demand for the efficient production of functional membrane proteins. In this context, cell-free protein synthesis represents a valuable alternative that allows for the high-throughput synthesis of functional membrane proteins. Here, we demonstrate the potential of our cell-free protein synthesis system, based on lysates from cultured Spodoptera frugiperda 21 cells, to produce pro- and eukaryotic membrane proteins with individual topological characteristics in an automated fashion. Analytical techniques, including confocal laser scanning microscopy, fluorescence detection of eYFP fusion proteins in a microplate reader and in-gel fluorescence of statistically incorporated fluorescent amino acid derivatives were employed. The reproducibility of our automated synthesis approach is underlined by coefficients of variation below 7.2%. Moreover, the functionality of the cell-free synthesized potassium channel KcsA was analyzed electrophysiologically. Finally, we expanded our cell-free membrane protein synthesis system by an orthogonal tRNA/synthetase pair for the site-directed incorporation of p-Azido-l-phenylalanine based on stop codon suppression. Incorporation was optimized by performance of a two-dimensional screening with different Mg(2+) and lysate concentrations. Subsequently, the selective modification of membrane proteins with incorporated p-Azido-l-phenylalanine was exemplified by Staudinger ligation with a phosphine-based fluorescence dye.
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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
| | - Oliver Kortt
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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38
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Brödel AK, Wüstenhagen DA, Kubick S. Cell-free protein synthesis systems derived from cultured mammalian cells. Methods Mol Biol 2015; 1261:129-40. [PMID: 25502197 DOI: 10.1007/978-1-4939-2230-7_7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a technology for the production of target proteins using novel cell-free systems derived from cultured human K562 cells and Chinese hamster ovary (CHO) cells. The protocol includes the cultivation of cells, the preparation of translationally active lysates, and the cell-free synthesis of desired proteins. An efficient expression vector based on the internal ribosome entry site (IRES) from the intergenic region (IGR) of the cricket paralysis virus (CrPV) was constructed for both systems. The coupled batch-based platforms enable the synthesis of a broad range of target proteins such as cytosolic proteins, secreted proteins, membrane proteins embedded into endogenous microsomes, and glycoproteins. The glycosylation of erythropoietin demonstrates the successful performance of posttranslational modifications in the novel cell-free systems. Protein yields of approximately 20 μg/ml (K562-based cell-free system) and 50 μg/ml (CHO-based cell-free system) of active firefly luciferase are obtained in the coupled transcription-translation systems within 3 h. As a result, both cell-free protein synthesis systems serve as powerful tools for high-throughput proteomics.
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Affiliation(s)
- Andreas K Brödel
- Department of Cell-free Bioproduction, 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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Dondapati SK, Kreir M, Quast RB, Wüstenhagen DA, Brüggemann A, Fertig N, Kubick S. Membrane assembly of the functional KcsA potassium channel in a vesicle-based eukaryotic cell-free translation system. Biosens Bioelectron 2014; 59:174-83. [DOI: 10.1016/j.bios.2014.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 10/25/2022]
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Developing cell-free protein synthesis systems: a focus on mammalian cells. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Stech M, Hust M, Schulze C, Dübel S, Kubick S. Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng Life Sci 2014; 14:387-398. [PMID: 25821419 PMCID: PMC4374706 DOI: 10.1002/elsc.201400036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 01/27/2023] Open
Abstract
Open cell-free translation systems based on Escherichia coli cell lysates have successfully been used to produce antibodies and antibody fragments. In this study, we demonstrate the cell-free expression of functional single-chain antibody variable fragments (scFvs) in a eukaryotic and endotoxin-free in vitro translation system based on Spodoptera frugiperda (Sf21) insect cell extracts. Three scFv candidates with different specificities were chosen as models. The first scFv candidate SH527-IIA4 specifically discriminates between its phosphorylated (SMAD2-P) and nonphosphorylated antigens (SMAD2) (where SMAD is mothers against decapentaplegic homolog 2), whereas the second scFv candidate SH527-IIC10 recognizes both, SMAD2-P and SMAD2. The third scFv candidate SH855-C11 binds specifically to a linear epitope of the CXC chemokine receptor type 5. The translocation of antibody fragments into the lumen of endogenous microsomal vesicles, which are contained in the lysate, was facilitated by fusion of scFv genes to the insect cell specific signal sequence of honeybee melittin. We compared the binding capabilities of scFv fragments with and without melittin signal peptide and detected that translocated scFv fragments were highly functional, whereas scFvs synthesized in the cytosol of the cell extract showed strongly decreased binding capabilities. Additionally, we describe a cell-free protein synthesis method for the incorporation of noncanonical amino acids into scFv molecules in eukaryotic cell lysates. We demonstrate the successful cotranslational labeling of de novo synthesized scFv molecules with fluorescent amino acids, using residue-specific as well as site-specific labeling.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Corina Schulze
- Department of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, University of Applied Sciences Berlin, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
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Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S. Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes. FEBS Lett 2014; 588:2774-81. [DOI: 10.1016/j.febslet.2014.06.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
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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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Stech M, Quast RB, Sachse R, Schulze C, Wüstenhagen DA, Kubick S. A continuous-exchange cell-free protein synthesis system based on extracts from cultured insect cells. PLoS One 2014; 9:e96635. [PMID: 24804975 PMCID: PMC4013096 DOI: 10.1371/journal.pone.0096635] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/09/2014] [Indexed: 11/22/2022] Open
Abstract
In this study, we present a novel technique for the synthesis of complex prokaryotic and eukaryotic proteins by using a continuous-exchange cell-free (CECF) protein synthesis system based on extracts from cultured insect cells. Our approach consists of two basic elements: First, protein synthesis is performed in insect cell lysates which harbor endogenous microsomal vesicles, enabling a translocation of de novo synthesized target proteins into the lumen of the insect vesicles or, in the case of membrane proteins, their embedding into a natural membrane scaffold. Second, cell-free reactions are performed in a two chamber dialysis device for 48 h. The combination of the eukaryotic cell-free translation system based on insect cell extracts and the CECF translation system results in significantly prolonged reaction life times and increased protein yields compared to conventional batch reactions. In this context, we demonstrate the synthesis of various representative model proteins, among them cytosolic proteins, pharmacological relevant membrane proteins and glycosylated proteins in an endotoxin-free environment. Furthermore, the cell-free system used in this study is well-suited for the synthesis of biologically active tissue-type-plasminogen activator, a complex eukaryotic protein harboring multiple disulfide bonds.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Robert B. Quast
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Rita Sachse
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Corina Schulze
- Beuth Hochschule für Technik Berlin - University of Applied Sciences Berlin, Life Sciences and Technology, Berlin, Germany
| | - Doreen A. Wüstenhagen
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
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Quast RB, Claussnitzer I, Merk H, Kubick S, Gerrits M. Synthesis and site-directed fluorescence labeling of azido proteins using eukaryotic cell-free orthogonal translation systems. Anal Biochem 2014; 451:4-9. [PMID: 24491444 DOI: 10.1016/j.ab.2014.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/17/2014] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
Abstract
Eukaryotic cell-free systems based on wheat germ and Spodoptera frugiperda insect cells were equipped with an orthogonal amber suppressor tRNA-synthetase pair to synthesize proteins with a site-specifically incorporated p-azido-l-phenylalanine residue in order to provide their chemoselective fluorescence labeling with azide-reactive dyes by Staudinger ligation. The specificity of incorporation and bioorthogonality of labeling within complex reaction mixtures was shown by means of translation and fluorescence detection of two model proteins: β-glucuronidase and erythropoietin. The latter contained the azido amino acid in proximity to a signal peptide for membrane translocation into endogenous microsomal vesicles of the insect cell-based system. The results indicate a stoichiometric incorporation of the azido amino acid at the desired position within the proteins. Moreover, the compatibility of cotranslational protein translocation, including glycosylation and amber suppression-based incorporation of p-azido-l-phenylalanine within a cell-free system, is demonstrated. The presented approach should be particularly useful for providing eukaryotic and membrane-associated proteins for investigation by fluorescence-based techniques.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, 14476 Potsdam, Germany
| | | | | | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, 14476 Potsdam, Germany
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Fenz SF, Sachse R, Schmidt T, Kubick S. Cell-free synthesis of membrane proteins: tailored cell models out of microsomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1382-8. [PMID: 24370776 DOI: 10.1016/j.bbamem.2013.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/27/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
Incorporation of proteins in biomimetic giant unilamellar vesicles (GUVs) is one of the hallmarks towards cell models in which we strive to obtain a better mechanistic understanding of the manifold cellular processes. The reconstruction of transmembrane proteins, like receptors or channels, into GUVs is a special challenge. This procedure is essential to make these proteins accessible to further functional investigation. Here we describe a strategy combining two approaches: cell-free eukaryotic protein expression for protein integration and GUV formation to prepare biomimetic cell models. The cell-free protein expression system in this study is based on insect lysates, which provide endoplasmic reticulum derived vesicles named microsomes. It enables signal-induced translocation and posttranslational modification of de novo synthesized membrane proteins. Combining these microsomes with synthetic lipids within the electroswelling process allowed for the rapid generation of giant proteo-liposomes of up to 50 μm in diameter. We incorporated various fluorescent protein-labeled membrane proteins into GUVs (the prenylated membrane anchor CAAX, the heparin-binding epithelial growth factor like factor Hb-EGF, the endothelin receptor ETB, the chemokine receptor CXCR4) and thus presented insect microsomes as functional modules for proteo-GUV formation. Single-molecule fluorescence microscopy was applied to detect and further characterize the proteins in the GUV membrane. To extend the options in the tailoring cell models toolbox, we synthesized two different membrane proteins sequentially in the same microsome. Additionally, we introduced biotinylated lipids to specifically immobilize proteo-GUVs on streptavidin-coated surfaces. We envision this achievement as an important first step toward systematic protein studies on technical surfaces.
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Affiliation(s)
- Susanne F Fenz
- Leiden Institute of Physics, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Rita Sachse
- Fraunhofer IBMT, Branch Potsdam-Golm, Group of Cell-free Protein Synthesis, Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Thomas Schmidt
- Leiden Institute of Physics, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Stefan Kubick
- Fraunhofer IBMT, Branch Potsdam-Golm, Group of Cell-free Protein Synthesis, Am Mühlenberg 13, 14476 Potsdam, Germany.
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Brödel AK, Sonnabend A, Roberts LO, Stech M, Wüstenhagen DA, Kubick S. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems. PLoS One 2013; 8:e82234. [PMID: 24376523 PMCID: PMC3869664 DOI: 10.1371/journal.pone.0082234] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 10/22/2013] [Indexed: 02/04/2023] Open
Abstract
Internal ribosome entry site (IRES) elements found in the 5′ untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR) of the Cricket paralysis virus (CrPV) genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established systems.
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Affiliation(s)
- Andreas K. Brödel
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Lisa O. Roberts
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Marlitt Stech
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Doreen A. Wüstenhagen
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT) Branch Potsdam-Golm, Potsdam, Germany
- * E-mail:
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Brödel AK, Sonnabend A, Kubick S. Cell‐free protein expression based on extracts from CHO cells. Biotechnol Bioeng 2013; 111:25-36. [DOI: 10.1002/bit.25013] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Andreas K. Brödel
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
| | - Andrei Sonnabend
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT)Branch Potsdam‐GolmAm Mühlenberg 1314476PotsdamGermany
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Cell-free Biosystems in the Production of Electricity and Bioenergy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:125-52. [PMID: 23748347 DOI: 10.1007/10_2013_201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
: Increasing needs of green energy and concerns of climate change are motivating intensive R&D efforts toward the low-cost production of electricity and bioenergy, such as hydrogen, alcohols, and jet fuel, from renewable sugars. Cell-free biosystems for biomanufacturing (CFB2) have been suggested as an emerging platform to replace mainstream microbial fermentation for the cost-effective production of some biocommodities. As compared to whole-cell factories, cell-free biosystems comprised of synthetic enzymatic pathways have numerous advantages, such as high product yield, fast reaction rate, broad reaction condition, easy process control and regulation, tolerance of toxic compound/product, and an unmatched capability of performing unnatural reactions. However, issues pertaining to high costs and low stabilities of enzymes and cofactors as well as compromised optimal conditions for different source enzymes need to be solved before cell-free biosystems are scaled up for biomanufacturing. Here, we review the current status of cell-free technology, update recent advances, and focus on its applications in the production of electricity and bioenergy.
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Bley T. A new generation of bioproduction systems. Eng Life Sci 2013. [DOI: 10.1002/elsc.201370012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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