1
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Bothe A, Ban N. A highly optimized human in vitro translation system. CELL REPORTS METHODS 2024; 4:100755. [PMID: 38608690 PMCID: PMC11046033 DOI: 10.1016/j.crmeth.2024.100755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
In vitro translation is an important method for studying fundamental aspects of co- and post-translational gene regulation, as well as for protein expression in the laboratory and on an industrial scale. Here, by re-examining and improving a human in vitro translation system (HITS), we were able to develop a minimal system where only four components are needed to supplement human cell lysates. Functional characterization of our improved HITS revealed the synergistic effect of mRNA capping and polyadenylation. Furthermore, we found that mRNAs are translated with an efficiency equal to or higher than existing state-of-the-art mammalian in vitro translation systems. Lastly, we present an easy preparation procedure for cytoplasmic extracts from cultured HeLa cells, which can be performed in any cell culture laboratory. These methodological advances will allow HITSs to become a widespread tool in basic molecular biology research.
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Affiliation(s)
- Adrian Bothe
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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2
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Machida K, Tanaka R, Miki S, Noseda S, Yuasa-Sunagawa M, Imataka H. High-throughput screening for a SARS-CoV-2 frameshifting inhibitor using a cell-free protein synthesis system. Biotechniques 2024; 76:161-168. [PMID: 38293767 DOI: 10.2144/btn-2023-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Programmed-1 ribosomal frameshifting (-1 PRF) is a translational mechanism adopted by some viruses, including SARS-CoV-2. To find a compound that can inhibit -1 PRF in SARS-CoV-2, we set up a high-throughput screening system using a HeLa cell extract-derived cell-free protein synthesis (CFPS) system. A total of 32,000 compounds were individually incubated with the CFPS system programmed with a -1 PRF-EGFP template. Several compounds were observed to decrease the -1 PRF-driven fluorescence, and one of them had some suppressive effect on -1 PRF of a SARS-CoV-2 genome sequence in transfected cells. Thus the CFPS system can be used as a tool for a high-throughput screening of chemicals.
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Affiliation(s)
- Kodai Machida
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
| | - Rin Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
| | - Seraya Miki
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
| | - Shotaro Noseda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
| | - Mayumi Yuasa-Sunagawa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
| | - Hiroaki Imataka
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, 671-2201, Japan
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3
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Aleksashin NA, Chang STL, Cate JHD. A highly efficient human cell-free translation system. RNA (NEW YORK, N.Y.) 2023; 29:1960-1972. [PMID: 37793791 PMCID: PMC10653386 DOI: 10.1261/rna.079825.123] [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: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells before cell lysate preparation significantly simplifies lysate preparation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. During in vitro translation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
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Affiliation(s)
- Nikolay A Aleksashin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Stacey Tsai-Lan Chang
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, USA
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4
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Aleksashin NA, Chang STL, Cate JHD. A highly efficient human cell-free translation system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527910. [PMID: 36798401 PMCID: PMC9934684 DOI: 10.1101/2023.02.09.527910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells significantly simplifies cell lysate preparation. The new CFPS system improves the translation of 5' cap-dependent mRNAs as well as those that use internal ribosome entry site (IRES) mediated translation initiation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. During in vitro translation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. We also find evidence for activation of regulatory pathways related to eukaryotic elongation factor 2 (eEF2) phosphorylation and ribosome quality control in the extracts. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
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Affiliation(s)
- Nikolay A. Aleksashin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Stacey Tsai-Lan Chang
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Jamie H. D. Cate
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, USA
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5
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Gurzeler LA, Ziegelmüller J, Mühlemann O, Karousis ED. Production of human translation-competent lysates using dual centrifugation. RNA Biol 2021; 19:78-88. [PMID: 34965175 PMCID: PMC8815625 DOI: 10.1080/15476286.2021.2014695] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein synthesis is a central process in gene expression and the development of efficient in vitro translation systems has been the focus of scientific efforts for decades. The production of translation-competent lysates originating from human cells or tissues remains challenging, mainly due to the variability of cell lysis conditions. Here we present a robust and fast method based on dual centrifugation that allows for detergent-free cell lysis under controlled mechanical forces. We optimized the lysate preparation to yield cytoplasm-enriched extracts from human cells that efficiently translate mRNAs in a cap-dependent as well as in an IRES-mediated way. Reduction of the phosphorylation state of eIF2α using recombinant GADD34 and 2-aminopurine considerably boosts the protein output, reinforcing the potential of this method to produce recombinant proteins from human lysates.
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Affiliation(s)
- Lukas-Adrian Gurzeler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jana Ziegelmüller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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6
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Makrydaki E, Marshall O, Heide C, Buldum G, Kontoravdi C, Polizzi KM. Cell-free protein synthesis using Chinese hamster ovary cells. Methods Enzymol 2021; 659:411-435. [PMID: 34752298 DOI: 10.1016/bs.mie.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell-free protein synthesis (CFPS) platforms can be used for rapid and flexible expression of proteins. The use of CFPS platforms from mammalian, specifically Chinese hamster ovary (CHO) cells, offers the possibility of a rapid prototyping platform for recombinant protein production with the capabilities of post-translational modifications. In this chapter, we discuss a refined CFPS system based on CHO cells, including: extract preparation, reaction mix composition, and accessory protein supplementation to enhance expression. Specifically, when the CHO cell extract is combined with a truncated version of GADD34 and K3L, stress-induced eIF2 phosphorylation is reduced and inhibition of translation initiation is relieved, increasing yields. A brief summary of the protocol for running the CFPS reactions is also described. Overall, the method is reliable and leads to a highly reproducible expression system. Finally, the advantages and disadvantages of the platform, in addition to expected outcomes, are also discussed.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Oscar Marshall
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Chiara Heide
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Gizem Buldum
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Cleo Kontoravdi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
| | - Karen M Polizzi
- Department of Chemical Engineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
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7
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Heide C, Buldum G, Moya-Ramirez I, Ces O, Kontoravdi C, Polizzi KM. Design, Development and Optimization of a Functional Mammalian Cell-Free Protein Synthesis Platform. Front Bioeng Biotechnol 2021; 8:604091. [PMID: 33604330 PMCID: PMC7884609 DOI: 10.3389/fbioe.2020.604091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/29/2020] [Indexed: 11/13/2022] Open
Abstract
In this paper, we describe the stepwise development of a cell-free protein synthesis (CFPS) platform derived from cultured Chinese hamster ovary (CHO) cells. We provide a retrospective summary of the design challenges we faced, and the optimized methods developed for the cultivation of cells and the preparation of translationally active lysates. To overcome low yields, we developed procedures to supplement two accessory proteins, GADD34 and K3L, into the reaction to prevent deactivation of the translational machinery by phosphorylation. We compared different strategies for implementing these accessory proteins including two variants of the GADD34 protein to understand the potential trade-offs between yield and ease of implementation. Addition of the accessory proteins increased yield of turbo Green Fluorescent Protein (tGFP) by up to 100-fold depending on which workflow was used. Using our optimized protocols as a guideline, users can successfully develop their own functional CHO CFPS system, allowing for broader application of mammalian CFPS.
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Affiliation(s)
- Chiara Heide
- Department of Chemical Engineering, Imperial College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom.,Imperial College Center for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Gizem Buldum
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Ignacio Moya-Ramirez
- Department of Chemical Engineering, Imperial College London, London, United Kingdom.,Imperial College Center for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Oscar Ces
- Department of Chemistry, Imperial College London, London, United Kingdom.,Institute of Chemical Biology, Imperial College London, London, United Kingdom
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, United Kingdom.,Imperial College Center for Synthetic Biology, Imperial College London, London, United Kingdom
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8
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Crespillo-Casado A, Claes Z, Choy MS, Peti W, Bollen M, Ron D. A Sephin1-insensitive tripartite holophosphatase dephosphorylates translation initiation factor 2α. J Biol Chem 2018; 293:7766-7776. [PMID: 29618508 PMCID: PMC5961032 DOI: 10.1074/jbc.ra118.002325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
The integrated stress response (ISR) is regulated by kinases that phosphorylate the α subunit of translation initiation factor 2 and phosphatases that dephosphorylate it. Genetic and biochemical observations indicate that the eIF2αP-directed holophosphatase, a therapeutic target in diseases of protein misfolding, is comprised of a regulatory subunit, PPP1R15, and a catalytic subunit, protein phosphatase 1 (PP1). In mammals, there are two isoforms of the regulatory subunit, PPP1R15A and PPP1R15B, with overlapping roles in the essential function of eIF2αP dephosphorylation. However, conflicting reports have appeared regarding the requirement for an additional co-factor, G-actin, in enabling substrate-specific dephosphorylation by PPP1R15-containing PP1 holoenzymes. An additional concern relates to the sensitivity of the holoenzyme to the [(o-chlorobenzylidene)amino]guanidines Sephin1 or guanabenz, putative small-molecule proteostasis modulators. It has been suggested that the source and method of purification of the PP1 catalytic subunit and the presence or absence of an N-terminal repeat–containing region in the PPP1R15A regulatory subunit might influence the requirement for G-actin and sensitivity of the holoenzyme to inhibitors. We found that eIF2αP dephosphorylation by PP1 was moderately stimulated by repeat-containing PPP1R15A in an unphysiological low ionic strength buffer, whereas stimulation imparted by the co-presence of PPP1R15A and G-actin was observed under a broad range of conditions, low and physiological ionic strength, regardless of whether the PPP1R15A regulatory subunit had or lacked the N-terminal repeat–containing region and whether it was paired with native PP1 purified from rabbit muscle or recombinant PP1 purified from bacteria. Furthermore, none of the PPP1R15A-containing holophosphatases tested were inhibited by Sephin1 or guanabenz.
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Affiliation(s)
- Ana Crespillo-Casado
- From the Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom,
| | - Zander Claes
- the Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium, and
| | - Meng S Choy
- the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041
| | - Wolfgang Peti
- the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041
| | - Mathieu Bollen
- the Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium, and
| | - David Ron
- From the Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom,
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9
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Majumder S, Willey PT, DeNies MS, Liu AP, Luxton GWG. A synthetic biology platform for the reconstitution and mechanistic dissection of LINC complex assembly. J Cell Sci 2018; 132:jcs.219451. [DOI: 10.1242/jcs.219451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/19/2018] [Indexed: 11/20/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) is a conserved nuclear envelope-spanning molecular bridge that is responsible for the mechanical integration of the nucleus with the cytoskeleton. LINC complexes are formed by a transluminal interaction between the outer and inner nuclear membrane KASH and SUN proteins, respectively. Despite recent structural insights, our mechanistic understanding of LINC complex assembly remains limited by the lack of an experimental system for its in vitro reconstitution and manipulation. Here, we describe artificial nuclear membranes (ANMs) as a synthetic biology platform based on mammalian cell-free expression for the rapid reconstitution of SUN proteins in supported lipid bilayers. We demonstrate that SUN1 and SUN2 are oriented in ANMs with solvent-exposed C-terminal KASH-binding SUN domains. We also find that SUN2 possesses a single transmembrane domain, while SUN1 possesses three. Finally, SUN protein-containing ANMs bind synthetic KASH peptides, thereby reconstituting the LINC complex core. This work represents the first in vitro reconstitution of KASH-binding SUN proteins in supported lipid bilayers using cell-free expression, which will be invaluable for testing proposed models of LINC complex assembly and its regulation.
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Affiliation(s)
- Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
| | - Patrick T. Willey
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maxwell S. DeNies
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48019, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48019, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48019, USA
| | - G. W. Gant Luxton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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10
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Svitkin YV, Cheng YM, Chakraborty T, Presnyak V, John M, Sonenberg N. N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. Nucleic Acids Res 2017; 45:6023-6036. [PMID: 28334758 PMCID: PMC5449617 DOI: 10.1093/nar/gkx135] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms. We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | | | | | | | | | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
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11
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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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12
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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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13
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Ho KKY, Murray VL, Liu AP. Engineering artificial cells by combining HeLa-based cell-free expression and ultrathin double emulsion template. Methods Cell Biol 2015; 128:303-18. [PMID: 25997354 DOI: 10.1016/bs.mcb.2015.01.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Generation of artificial cells provides the bridge needed to cover the gap between studying the complexity of biological processes in whole cells and studying these same processes in an in vitro reconstituted system. Artificial cells are defined as the encapsulation of biologically active material in a biological or synthetic membrane. Here, we describe a robust and general method to produce artificial cells for the purpose of mimicking one or more behaviors of a cell. A microfluidic double emulsion system is used to encapsulate a mammalian cell-free expression system that is able to express membrane proteins into the bilayer or soluble proteins inside the vesicles. The development of a robust platform that allows the assembly of artificial cells is valuable in understanding subcellular functions and emergent behaviors in a more cell-like environment as well as for creating novel signaling pathways to achieve specific cellular behaviors.
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Affiliation(s)
- Kenneth K Y Ho
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Victoria L Murray
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Biophysics Program, University of Michigan, Ann Arbor, MI, USA
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14
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Strategies to make protein serine/threonine (PP1, calcineurin) and tyrosine phosphatases (PTP1B) druggable: achieving specificity by targeting substrate and regulatory protein interaction sites. Bioorg Med Chem 2015; 23:2781-5. [PMID: 25771485 DOI: 10.1016/j.bmc.2015.02.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 12/18/2022]
Abstract
The established dogma is that protein serine/threonine (PSPs) and tyrosine (PTPs) phosphatases are unattainable drug targets. This is because natural product inhibitors of PSP active sites are lethal, while the active sites of PTPs are exceptionally conserved and charged, making it nearly impossible to develop PTP inhibitors that are selective. However, due to a series of recent structural and functional studies, this view of phosphatases is about to undergo a radical change. Rather than target active sites, these studies have demonstrated that targeting PSP/PTP protein (substrate/regulatory) interaction sites, which are distal from the active sites, are highly viable and suitable drugs targets. This is especially true for calcineurin (CN), in which the blockbuster immunosuppressant drugs FK506 and cyclosporin A were recently demonstrated to bind and block one of the key CN substrate interaction sites, the LxVP site. Additional studies show that this approach-targeting substrate and/or regulatory protein interaction sites-also holds incredible promise for protein phosphatase 1 (PP1)-related diseases. Finally, domains outside PTP catalytic domains have also recently been demonstrated to directly alter PTP activity. Collectively, these novel insights offer new, transformative perspectives for the therapeutic targeting of PSPs by interfering with the binding of PIPs or substrates and PTPs by targeting allosteric sites outside their catalytic domains.
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Machida K, Mikami S, Masutani M, Mishima K, Kobayashi T, Imataka H. A translation system reconstituted with human factors proves that processing of encephalomyocarditis virus proteins 2A and 2B occurs in the elongation phase of translation without eukaryotic release factors. J Biol Chem 2014; 289:31960-31971. [PMID: 25258322 PMCID: PMC4231674 DOI: 10.1074/jbc.m114.593343] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The genomic RNA of encephalomyocarditis virus (EMCV) encodes a single polyprotein, and the primary scission of the polyprotein occurs between nonstructural proteins 2A and 2B by an unknown mechanism. To gain insight into the mechanism of 2A-2B processing, we first translated the 2A-2B region in vitro with eukaryotic and prokaryotic translation systems. The 2A-2B processing occurred only in the eukaryotic systems, not in the prokaryotic systems, and the unprocessed 2A-2B protein synthesized by a prokaryotic system remained uncleaved when incubated with a eukaryotic cell extract. These results suggest that 2A-2B processing is a eukaryote-specific, co-translational event. To define the translation factors required for 2A-2B processing, we constituted a protein synthesis system with eukaryotic elongation factors 1 and 2, eukaryotic release factors 1 and 3 (eRF1 and eRF3), aminoacyl-tRNA synthetases, tRNAs, ribosome subunits, and a plasmid template that included the hepatitis C virus internal ribosome entry site. We successfully reproduced 2A-2B processing in the reconstituted system even without eRFs. Our results indicate that this unusual event occurs in the elongation phase of translation.
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Affiliation(s)
- Kodai Machida
- Department of Materials Science and Chemistry and University of Hyogo, Himeji 671-2201, Japan; Molecular Nanotechnology Research Center, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan and
| | - Satoshi Mikami
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan
| | - Mamiko Masutani
- Department of Materials Science and Chemistry and University of Hyogo, Himeji 671-2201, Japan
| | - Kurumi Mishima
- Department of Materials Science and Chemistry and University of Hyogo, Himeji 671-2201, Japan
| | - Tominari Kobayashi
- Department of Materials Science and Chemistry and University of Hyogo, Himeji 671-2201, Japan
| | - Hiroaki Imataka
- Department of Materials Science and Chemistry and University of Hyogo, Himeji 671-2201, Japan; Molecular Nanotechnology Research Center, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan and.
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Kobayashi T, Machida K, Imataka H. Human cell extract-derived cell-free systems for virus synthesis. Methods Mol Biol 2014; 1118:149-56. [PMID: 24395414 DOI: 10.1007/978-1-62703-782-2_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell-free synthesis of an infectious virus is an ideal tool for elucidating the mechanism of viral replication and for development of antiviral drugs. In this chapter, the synthesis of Encephalomyocarditis virus (EMCV) from RNA and DNA in a HeLa cell extract-derived in vitro protein expression system is described. When a synthetic EMCV RNA with a hammerhead ribozyme sequence at its 5'-end is incubated with a HeLa cell extract using a dialysis system, EMCV particles are progressively synthesized. For EMCV synthesis from DNA, a plasmid harboring the full-length cDNA of EMCV with the T7 promoter/terminator unit is incubated in the HeLa cell extract supplemented with T7 RNA polymerase.
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Affiliation(s)
- Tominari Kobayashi
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
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Masutani M, Machida K, Kobayashi T, Yokoyama S, Imataka H. Reconstitution of eukaryotic translation initiation factor 3 by co-expression of the subunits in a human cell-derived in vitro protein synthesis system. Protein Expr Purif 2013; 87:5-10. [DOI: 10.1016/j.pep.2012.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 12/29/2022]
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Purification and visualization of encephalomyocarditisvirus synthesized by an in vitro protein expression system derived from mammalian cell extract. Biotechnol Lett 2012; 35:309-14. [DOI: 10.1007/s10529-012-1086-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
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Kobayashi T, Nakamura Y, Mikami S, Masutani M, Machida K, Imataka H. Synthesis of encephalomyocarditis virus in a cell-free system: from DNA to RNA virus in one tube. Biotechnol Lett 2011; 34:67-73. [DOI: 10.1007/s10529-011-0744-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/16/2011] [Indexed: 11/29/2022]
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