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Ogawa A, Fujikawa M, Onishi K, Takahashi H. Cell-Free Biosensors Based on Modular Eukaryotic Riboswitches That Function in One Pot at Ambient Temperature. ACS Synth Biol 2024; 13:2238-2245. [PMID: 38913391 DOI: 10.1021/acssynbio.4c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Artificial riboswitches responsive to user-defined analytes can be constructed by successfully inserting in vitro selected aptamers, which bind to the analytes, into untranslated regions of mRNA. Among them, eukaryotic riboswitches are more promising as biosensors than bacterial ones because they function well at ambient temperature. In addition, cell-free expression systems allow the broader use of these riboswitches as cell-free biosensors in an environmentally friendly manner without cellular limitations. The current best cell-free eukaryotic riboswitch regulates eukaryotic canonical translation initiation through self-cleavage mediated by an implanted analyte-responsive ribozyme (i.e., an aptazyme, an aptamer-ribozyme fusion). However, it has critical flaws as a sensor: due to the less-active ribozyme used, self-cleavage and translation reactions must be conducted separately and sequentially, and a different aptazyme has to be selected to change the analyte specificity, even if an aptamer for the next analyte is available. We here stepwise engineered novel types of cell-free eukaryotic riboswitches that harness highly active self-cleavage and thus require no reaction partitioning. Despite the single-step and one-pot reaction, these riboswitches showed higher analyte dose dependency and sensitivities than the current best cell-free eukaryotic riboswitch requiring multistep reactions. In addition, the analyte specificity can be changed in an extremely facile way, simply by aptamer substitution (and the subsequent simple fine-tuning for giant aptamers). Given that cell-free systems can be lyophilized for storage and transport, the present one-pot and thus easy-to-handle cell-free biosensors utilizing eukaryotic riboswitches are expected to be widely used for on-the-spot sensing of analytes at ambient temperature.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Masahiro Fujikawa
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Kazuki Onishi
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
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2
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Takahashi H, Ogawa A. Coupled in vitro transcription/translation based on wheat germ extract for efficient expression from PCR-generated templates in short-time batch reactions. Bioorg Med Chem Lett 2021; 52:128412. [PMID: 34634474 DOI: 10.1016/j.bmcl.2021.128412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
We successfully constructed a coupled in vitro transcription/translation (cIVTT) system based on wheat germ extract (WGE) for efficient expression from PCR-generated DNA templates in short-time (∼3-h) batch reactions. The productivity of this system under optimized conditions was 85 μg (2.8 nmol) per 1 mL of reaction solution (corresponding to 425 μg per 1 mL of WGE), which was about 9-fold higher than that by the conventional batch method using mRNA as a template. The DNA template concentration required for efficient cIVTT was as low as 2.5 nM, which is much lower than those required for other eukaryotic cIVTT systems to maximize their productivity (30-50 nM). The productivity of the present system with a 2.5 nM template was 80-fold and 4-fold higher than that of a commercially available WGE-based cIVTT system with a 2.5 nM and a 40 nM template, respectively. In addition, the present system functioned well in a liposome (i.e., in an artificial cell) without a loss of productivity. Given that WGE-based systems have the advantage of being suitable for the expression of a broad range of proteins, the present cIVTT system is expected to be widely used in future cell-free synthetic biology.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
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3
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Takahashi H, Ogawa A. A Detailed Protocol for Preparing Millimeter-sized Supergiant Liposomes that Permit Efficient Eukaryotic Cell-free Translation in the Interior. Bio Protoc 2021; 11:e4054. [PMID: 34262997 DOI: 10.21769/bioprotoc.4054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/02/2022] Open
Abstract
Liposomes have been used as a pseudo cell membrane for encapsulating biomolecules and creating an artificial cell in the interior where biochemical reactions can occur. Among the several methods used to prepare biomolecule-encapsulating liposomes, the spontaneous emulsion transfer method is superior to others in that it allows us to readily prepare relatively large liposomes whose sizes are controlled (from micrometer- to millimeter-sized liposomes) without special equipment. However, conventional protocols for this method require liposomes to contain a considerably high concentration of sucrose (high-density solute), which severely inhibits gene expression, one of the most important biochemical reactions. Thus, we optimized the preparation conditions to develop a wheat germ extract (WGE)-based protocol that requires a much lower concentration of sucrose and has almost no effect on eukaryotic cell-free translation. Our protocol allows us to successfully prepare millimeter-sized, moderately stable, WGE-encapsulating liposomes in which WGE translation takes place efficiently. Since a broad range of genes derived from various types of organisms can be efficiently translated in a WGE-based translation system, liposomes prepared using our protocol would be useful as a versatile research tool for artificial cells.
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Affiliation(s)
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan
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4
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Abstract
A nonsense suppressor tRNA (sup-tRNA) allows a natural or non-natural amino acid to be assigned to a nonsense codon in mRNA. Sup-tRNAs were utilized initially for studying tRNA functions but lately are used more for protein engineering and gene regulation. In the latter application, a sup-tRNA that is aminoacylated with a natural amino acid by the corresponding aminoacyl-tRNA synthetase is used to express a full-length natural protein from its mutated gene with a nonsense codon in the middle. This type of sup-tRNA has recently been artificially evolved to develop biosensors. In these biosensors, an analyte induces the processing of an engineered premature sup-tRNA into a mature sup-tRNA, which suppresses the corresponding nonsense codon incorporated into a gene, encoding an easily detectable reporter protein. This review introduces sup-tRNA-based biosensors that the author's group has developed by utilizing bacterial and eukaryotic cell-free translation systems.
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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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6
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Chiba CH, Knirsch MC, Azzoni AR, Moreira AR, Stephano MA. Cell-free protein synthesis: advances on production process for biopharmaceuticals and immunobiological products. Biotechniques 2021; 70:126-133. [PMID: 33467890 DOI: 10.2144/btn-2020-0155] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biopharmaceutical products are of great importance in the treatment or prevention of many diseases and represent a growing share of the global pharmaceutical market. The usual technology for protein synthesis (cell-based expression) faces certain obstacles, especially with 'difficult-to-express' proteins. Cell-free protein synthesis (CFPS) can overcome the main bottlenecks of cell-based expression. This review aims to present recent advances in the production process of biologic products by CFPS. First, key aspects of CFPS systems are summarized. A description of several biologic products that have been successfully produced using the CFPS system is provided. Finally, the CFPS system's ability to scale up and scale down, its main limitations and its application for biologics production are discussed.
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Affiliation(s)
- Camila Hiromi Chiba
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Marcos Camargo Knirsch
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Adriano Rodrigues Azzoni
- Departamento de Engenharia Química, Escola Politécnica, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio R Moreira
- Department of Chemical, Biochemical & Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Marco Antonio Stephano
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
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7
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Takahashi H, Ogawa A. Preparation of a Millimeter-Sized Supergiant Liposome That Allows for Efficient, Eukaryotic Cell-Free Translation in the Interior by Spontaneous Emulsion Transfer. ACS Synth Biol 2020; 9:1608-1614. [PMID: 32559381 DOI: 10.1021/acssynbio.0c00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We sought to prepare millimeter-sized supergiant unilamellar vesicles (SGUVs) by spontaneous emulsion transfer for efficient, eukaryotic cell-free translation in the interior. Although the conventional protocols require that a considerably high concentration of sucrose be encapsulated into the SGUVs for their efficient formation, such high amounts of sucrose severely inhibited cell-free translation based on wheat germ extract (WGE). We thus optimized the preparation conditions to permit SGUV formation at a much lower concentration of sucrose that has almost no effect on WGE translation. Under the optimized conditions, we successfully prepared WGE translation system-encapsulating SGUVs that allow for protein synthesis with a high efficiency comparable to that outside a liposome. The optimization also resulted in a high rate of successful SGUV formation (>90%) and a decent stability of the formed SGUVs (>60 min). These SGUVs are expected to serve as research tools in cell-free synthetic biology and as foundations for artificial cell-based biosensors.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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8
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Mutation of the start codon to enhance Cripavirus internal ribosome entry site-mediated translation in a wheat germ extract. Bioorg Med Chem Lett 2019; 29:126729. [PMID: 31607608 DOI: 10.1016/j.bmcl.2019.126729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/22/2022]
Abstract
Wheat germ extract (WGE) is one of the most widely used eukaryotic cell-free translation systems for easy synthesis of a broad range of proteins merely by adding template mRNAs. Its productivity has thus far been improved by removing translational inhibitors from the extract and stabilizing the template with terminal protectors. Nonetheless, there remains room for increasing the yield by designing a terminally protected template with higher susceptibility to translation. Given the fact that a 5' terminal protector is a strong inhibitor of the canonical translation, we herein focused on Cripavirus internal ribosome entry sites (IRESes), which allow for a unique translation initiation from a non-AUG start codon without the help of any initiation factors. We mutated their start codons to enhance the IRES-mediated translation efficiency in WGE. One of the mutants showed considerably higher efficiency, 3-4-fold higher than that of its wild type, and also 3-4-fold higher than the canonical translation efficiency by an IRES-free mRNA having one of the most effective canonical-translation enhancers. Because this mutated IRES is compatible with different types of genes and terminal protectors, we expect it will be widely used to synthesize proteins in WGE.
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9
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In vitro selection of a 3′ terminal short protector that stabilizes transcripts to improve the translation efficiency in a wheat germ extract. Bioorg Med Chem Lett 2019; 29:2141-2144. [DOI: 10.1016/j.bmcl.2019.06.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 11/24/2022]
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10
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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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11
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Ntege EH, Takashima E, Morita M, Nagaoka H, Ishino T, Tsuboi T. Blood-stage malaria vaccines: post-genome strategies for the identification of novel vaccine candidates. Expert Rev Vaccines 2017; 16:769-779. [PMID: 28604122 DOI: 10.1080/14760584.2017.1341317] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION An efficacious malaria vaccine is necessary to advance the current control measures towards malaria elimination. To-date, only RTS,S/AS01, a leading pre-erythrocytic stage vaccine completed phase 3 trials, but with an efficacy of 28-36% in children, and 18-26% in infants, that waned over time. Blood-stage malaria vaccines protect against disease, and are considered effective targets for the logical design of next generation vaccines to improve the RTS,S field efficacy. Therefore, novel blood-stage vaccine candidate discovery efforts are critical, albeit with several challenges including, high polymorphisms in vaccine antigens, poor understanding of targets of naturally protective immunity, and difficulties in the expression of high AT-rich plasmodial proteins. Areas covered: PubMed ( www.ncbi.nlm.nih.gov/pubmed ) was searched to review the progress and future prospects of malaria vaccine research and development. We focused on post-genome vaccine candidate discovery, malaria vaccine development, sequence diversity, pre-clinical and clinical trials. Expert commentary: Post-genome high-throughput technologies using wheat germ cell-free protein synthesis technology and immuno-profiling with sera from malaria patients with clearly defined outcomes are highlighted to overcome current challenges of malaria vaccine candidate discovery.
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Affiliation(s)
- Edward H Ntege
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Eizo Takashima
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Masayuki Morita
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Hikaru Nagaoka
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Tomoko Ishino
- b Division of Molecular Parasitology , Proteo-Science Center, Ehime University , Toon , Ehime , Japan
| | - Takafumi Tsuboi
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
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12
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Minkoff BB, Makino SI, Haruta M, Beebe ET, Wrobel RL, Fox BG, Sussman MR. A cell-free method for expressing and reconstituting membrane proteins enables functional characterization of the plant receptor-like protein kinase FERONIA. J Biol Chem 2017; 292:5932-5942. [PMID: 28235802 DOI: 10.1074/jbc.m116.761981] [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: 10/04/2016] [Revised: 02/09/2017] [Indexed: 01/17/2023] Open
Abstract
There are more than 600 receptor-like kinases (RLKs) in Arabidopsis, but due to challenges associated with the characterization of membrane proteins, only a few have known biological functions. The plant RLK FERONIA is a peptide receptor and has been implicated in plant growth regulation, but little is known about its molecular mechanism of action. To investigate the properties of this enzyme, we used a cell-free wheat germ-based expression system in which mRNA encoding FERONIA was co-expressed with mRNA encoding the membrane scaffold protein variant MSP1D1. With the addition of the lipid cardiolipin, assembly of these proteins into nanodiscs was initiated. FERONIA protein kinase activity in nanodiscs was higher than that of soluble protein and comparable with other heterologously expressed protein kinases. Truncation experiments revealed that the cytoplasmic juxtamembrane domain is necessary for maximal FERONIA activity, whereas the transmembrane domain is inhibitory. An ATP analogue that reacts with lysine residues inhibited catalytic activity and labeled four lysines; mutagenesis demonstrated that two of these, Lys-565 and Lys-663, coordinate ATP in the active site. Mass spectrometric phosphoproteomic measurements further identified phosphorylation sites that were examined using phosphomimetic mutagenesis. The results of these experiments are consistent with a model in which kinase-mediated phosphorylation within the C-terminal region is inhibitory and regulates catalytic activity. These data represent a step further toward understanding the molecular basis for the protein kinase catalytic activity of FERONIA and show promise for future characterization of eukaryotic membrane proteins.
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Affiliation(s)
- Benjamin B Minkoff
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Miyoshi Haruta
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | | | - Michael R Sussman
- From the Department of Biochemistry and .,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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13
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Hunt JP, Yang SO, Wilding KM, Bundy BC. The growing impact of lyophilized cell-free protein expression systems. Bioengineered 2016; 8:325-330. [PMID: 27791452 DOI: 10.1080/21655979.2016.1241925] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recently reported shelf-stable, on-demand protein synthesis platforms are enabling new possibilities in biotherapeutics, biosensing, biocatalysis, and high throughput protein expression. Lyophilized cell-free protein expression systems not only overcome cold-storage limitations, but also enable stockpiling for on-demand synthesis and completely sterilize the protein synthesis platform. Recently reported high-yield synthesis of cytotoxic protein Onconase from lyophilized E. coli extract preparations demonstrates the utility of lyophilized cell-free protein expression and its potential for creating on-demand biotherapeutics, vaccines, biosensors, biocatalysts, and high throughput protein synthesis.
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Affiliation(s)
- J Porter Hunt
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Seung Ook Yang
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Kristen M Wilding
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Bradley C Bundy
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
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14
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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: 40] [Impact Index Per Article: 5.0] [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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15
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Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol 2015; 3:165. [PMID: 26579511 PMCID: PMC4621489 DOI: 10.3389/fbioe.2015.00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022] Open
Abstract
Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Christopher M Bianchetti
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Chemistry, University of Wisconsin-Oshkosh , Oshkosh, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin-Madison , Madison, WI , USA
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16
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Tan BH, Suzuki Y, Takahashi H, Ying PHR, Takahashi C, Han Q, Chin WX, Chao SH, Sawasaki T, Yamamoto N, Suzuki Y. Identification of RFPL3 protein as a novel E3 ubiquitin ligase modulating the integration activity of human immunodeficiency virus, type 1 preintegration complex using a microtiter plate-based assay. J Biol Chem 2014; 289:26368-26382. [PMID: 25107902 DOI: 10.1074/jbc.m114.561662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Integration, one of the hallmarks of retrovirus replication, is mediated by a nucleoprotein complex called the preintegration complex (PIC), in which viral DNA is associated with many protein components that are required for completion of the early phase of infection. A striking feature of the PIC is its powerful integration activity in vitro. The PICs from a freshly isolated cytoplasmic extract of infected cells are able to insert viral DNA into exogenously added target DNA in vitro. Therefore, a PIC-based in vitro assay is a reliable system for assessing protein factors influencing retroviral integration. In this study, we applied a microtiter plate-based in vitro assay to a screening study using a protein library that was produced by the wheat germ cell-free protein synthesis system. Using a library of human E3 ubiquitin ligases, we identified RFPL3 as a potential stimulator of human immunodeficiency virus, type 1 (HIV-1) PIC integration activity in vitro. This enhancement of PIC activity by RFPL3 was likely to be attributed to its N-terminal RING domain. To further understand the functional role of RFPL3 in HIV infection, we created a human cell line overexpressing RFPL3. Immunoprecipitation analysis revealed that RFPL3 was associated with the human immunodeficiency virus, type 1 PICs in infected cells. More importantly, single-round HIV-1 infection was enhanced significantly by RFPL3 expression. Our proteomic approach displays an advantage in the identification of new cellular proteins affecting the integration activity of the PIC and, therefore, contributes to the understanding of functional interaction between retroviral integration complexes and host factors.
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Affiliation(s)
- Beng Hui Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Yasutsugu Suzuki
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Hirotaka Takahashi
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Pamela Ho Rui Ying
- Veterinary Bioscience, Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Chikako Takahashi
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Qi'En Han
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Wei Xin Chin
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore
| | - Sheng-Hao Chao
- Expression Engineering Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Tatsuya Sawasaki
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan, and
| | - Naoki Yamamoto
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore,.
| | - Youichi Suzuki
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, #15-02, Singapore 117599, Singapore,; Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
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17
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Ogawa A, Tabuchi J, Doi Y. Identification of short untranslated regions that sufficiently enhance translation in high-quality wheat germ extract. Bioorg Med Chem Lett 2014; 24:3724-7. [PMID: 25037913 DOI: 10.1016/j.bmcl.2014.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 10/25/2022]
Abstract
High-quality wheat germ extract (hqWGE) is very useful for the high-yield production of various types of protein. The most important key to high productivity is the design of mRNA templates. Although the design has been refined for straightforward and efficient translation in hqWGE, there is still room for improvement in untranslated regions (UTRs), especially the 3' UTR length, because a long, cumbersome 3' UTR is commonly used for translation enhancement. Here we examined some short viral 3' cap-independent translation enhancers (3' CITEs) to identify effective ones for efficient translation in hqWGE. We then combined the most effective 3' CITE and a 5' enhancer to further increase the translation efficiency. mRNA with the optimal short 3' and 5' UTRs, both of whose length was less than 150 nt, exhibited a productivity of 1.4 mg/mL in prolonged large-scale protein synthesis in hqWGE, which was comparable to that of control mRNA with a commonly-used long 3' UTR (∼1200 nt).
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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18
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Sierecki E, Giles N, Polinkovsky M, Moustaqil M, Alexandrov K, Gambin Y. A cell-free approach to accelerate the study of protein-protein interactions in vitro. Interface Focus 2014; 3:20130018. [PMID: 24511386 DOI: 10.1098/rsfs.2013.0018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein-protein interactions are highly desirable targets in drug discovery, yet only a fraction of drugs act as binding inhibitors. Here, we review the different technologies used to find and validate protein-protein interactions. We then discuss how the novel combination of cell-free protein expression, AlphaScreen and single-molecule fluorescence spectroscopy can be used to rapidly map protein interaction networks, determine the architecture of protein complexes, and find new targets for drug discovery.
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Affiliation(s)
- E Sierecki
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
| | - N Giles
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
| | - M Polinkovsky
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
| | - M Moustaqil
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
| | - K Alexandrov
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
| | - Y Gambin
- Institute for Molecular Bioscience , University of Queensland , Saint Lucia, Queensland , Australia
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19
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Sierecki E, Stevers LM, Giles N, Polinkovsky ME, Moustaqil M, Mureev S, Johnston WA, Dahmer-Heath M, Skalamera D, Gonda TJ, Gabrielli B, Collins BM, Alexandrov K, Gambin Y. Rapid mapping of interactions between Human SNX-BAR proteins measured in vitro by AlphaScreen and single-molecule spectroscopy. Mol Cell Proteomics 2014; 13:2233-45. [PMID: 24866125 DOI: 10.1074/mcp.m113.037275] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein dimerization and oligomerization is commonly used by nature to increase the structural and functional complexity of proteins. Regulated protein assembly is essential to transfer information in signaling, transcriptional, and membrane trafficking events. Here we show that a combination of cell-free protein expression, a proximity based interaction assay (AlphaScreen), and single-molecule fluorescence allow rapid mapping of homo- and hetero-oligomerization of proteins. We have applied this approach to the family of BAR domain-containing sorting nexin (SNX-BAR) proteins, which are essential regulators of membrane trafficking and remodeling in all eukaryotes. Dimerization of BAR domains is essential for creating a concave structure capable of sensing and inducing membrane curvature. We have systematically mapped 144 pairwise interactions between the human SNX-BAR proteins and generated an interaction matrix of preferred dimerization partners for each family member. We find that while nine SNX-BAR proteins are able to form homo-dimers, several including the retromer-associated SNX1, SNX2, and SNX5 require heteromeric interactions for dimerization. SNX2, SNX4, SNX6, and SNX8 show a promiscuous ability to bind other SNX-BAR proteins and we also observe a novel interaction with the SNX3 protein which lacks the BAR domain structure.
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Affiliation(s)
- Emma Sierecki
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Loes M Stevers
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Nichole Giles
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Mark E Polinkovsky
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Mehdi Moustaqil
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Sergey Mureev
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Wayne A Johnston
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Mareike Dahmer-Heath
- §University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Dubravka Skalamera
- §University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Thomas J Gonda
- ¶School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Brian Gabrielli
- §University of Queensland, Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - Brett M Collins
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Kirill Alexandrov
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia;
| | - Yann Gambin
- From the ‡Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
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20
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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21
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Lyophilized Escherichia coli-based cell-free systems for robust, high-density, long-term storage. Biotechniques 2014; 56:186-93. [DOI: 10.2144/000114158] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 11/23/2022] Open
Abstract
Cell-free protein synthesis (CFPS) is a versatile tool for rapid recombinant protein production and engineering. One drawback of cell-free technology is the necessity to store the major components—cell extracts and energy systems—below freezing in bulky aqueous solutions. Here we describe simple methods for lyophilizing extracts and preparing powdered energy systems for CFPS. These techniques allow for high-density storage of cell-free systems that are more robust against temperature and bacterial degradation. Our methods have the potential to decrease storage expenses, allow for longer shelf-life of cell extracts at room temperature, and enable durable portable protein production technologies.
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22
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Diamante L, Gatti-Lafranconi P, Schaerli Y, Hollfelder F. In vitro affinity screening of protein and peptide binders by megavalent bead surface display. Protein Eng Des Sel 2013; 26:713-24. [PMID: 23980186 PMCID: PMC3785251 DOI: 10.1093/protein/gzt039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/30/2013] [Accepted: 07/02/2013] [Indexed: 11/12/2022] Open
Abstract
The advent of protein display systems has provided access to tailor-made protein binders by directed evolution. We introduce a new in vitro display system, bead surface display (BeSD), in which a gene is mounted on a bead via strong non-covalent (streptavidin/biotin) interactions and the corresponding protein is displayed via a covalent thioether bond on the DNA. In contrast to previous monovalent or low-copy bead display systems, multiple copies of the DNA and the protein or peptide of interest are displayed in defined quantities (up to 10(6) of each), so that flow cytometry can be used to obtain a measure of binding affinity. The utility of the BeSD in directed evolution is validated by library selections of randomized peptide sequences for binding to the anti-hemagglutinin (HA) antibody that proceed with enrichments in excess of 10(3) and lead to the isolation of high-affinity HA-tags within one round of flow cytometric screening. On-bead K(d) measurements suggest that the selected tags have affinities in the low nanomolar range. In contrast to other display systems (such as ribosome, mRNA and phage display) that are limited to affinity panning selections, BeSD possesses the ability to screen and rank binders by their affinity in vitro, a feature that hitherto has been exclusive to in vivo multivalent cell display systems (such as yeast display).
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Affiliation(s)
| | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
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23
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Maslennikov I, Choe S. Advances in NMR structures of integral membrane proteins. Curr Opin Struct Biol 2013; 23:555-62. [PMID: 23721747 DOI: 10.1016/j.sbi.2013.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/26/2013] [Accepted: 05/01/2013] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins (IMPs) play a central role in cell communication with the environment. Their structures are essential for our understanding of the molecular mechanisms of signaling and for drug design, yet they remain badly underrepresented in the protein structure databank. Solution NMR is, aside from X-ray crystallography, the major tool in structural biology. Here we review recently reported solution NMR structures of polytopic IMPs and discuss the new approaches, which were developed in the course of these studies to overcome barriers in the field. Advances in cell-free protein expression, combinatorial isotope labeling, resonance assignment, and collection of structural data greatly accelerated IMP structure determination by solution NMR. In addition, novel membrane-mimicking media made possible determination of solution NMR structures of IMPs in a native-like lipid environment.
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24
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Li J, Han ET. Dissection of the Plasmodium vivax reticulocyte binding-like proteins (PvRBPs). Biochem Biophys Res Commun 2012; 426:1-6. [DOI: 10.1016/j.bbrc.2012.08.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 08/11/2012] [Indexed: 01/08/2023]
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25
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Wang Y, Xu W, Kou X, Luo Y, Zhang Y, Ma B, Wang M, Huang K. Establishment and optimization of a wheat germ cell-free protein synthesis system and its application in venom kallikrein. Protein Expr Purif 2012; 84:173-80. [PMID: 22626528 DOI: 10.1016/j.pep.2012.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 12/18/2022]
Abstract
Wheat germ cell-free protein synthesis systems have the potential to synthesize functional proteins safely and with high accuracy, but the poor energy supply and the instability of mRNA templates reduce the productivity of this system, which restricts its applications. In this report, phosphocreatine and pyruvate were added to the system to supply ATP as a secondary energy source. After comparing the protein yield, we found that phosphocreatine is more suitable for use in the wheat germ cell-free protein synthesis system. To stabilize the mRNA template, the plasmid vector, SP6 RNA polymerase, and Cu(2+) were optimized, and a wheat germ cell-free protein synthesis system with high yield and speed was established. When plasmid vector (30 ng/μl), SP6 RNA polymerase (15 U), phosphocreatine (25 mM), and Cu(2+) (5 mM) were added to the system and incubated at 26°C for 16 h, the yield of venom kallikrein increased from 0.13 to 0.74 mg/ml. The specific activity of the recombinant protein was 1.3 U/mg, which is only slightly lower than the crude venom kallikrein (1.74 U/mg) due to the lack of the sugar chain. In this study, the yield of venom kallikrein was improved by optimizing the system, and a good foundation has been laid for industrial applications and for further studies.
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Affiliation(s)
- Yunpeng Wang
- School of Chemical Engineering and Technology, Tianjin University Tianjin 300072, China
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26
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Luo Z, Zhang S. Designer nanomaterials using chiral self-assembling peptide systems and their emerging benefit for society. Chem Soc Rev 2012; 41:4736-54. [DOI: 10.1039/c2cs15360b] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Ge X, Luo D, Xu J. Cell-free protein expression under macromolecular crowding conditions. PLoS One 2011; 6:e28707. [PMID: 22174874 PMCID: PMC3234285 DOI: 10.1371/journal.pone.0028707] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 11/14/2011] [Indexed: 01/29/2023] Open
Abstract
Background Cell-free protein expression (CFPE) comprised of in vitro transcription and translation is currently manipulated in relatively dilute solutions, in which the macromolecular crowding effects present in living cells are largely ignored. This may not only affect the efficiency of protein synthesis in vitro, but also limit our understanding of the functions and interactions of biomolecules involved in this fundamental biological process. Methodology/Principal Findings Using cell-free synthesis of Renilla luciferase in wheat germ extract as a model system, we investigated the CFPE under macromolecular crowding environments emulated with three different crowding agents: PEG-8000, Ficoll-70 and Ficoll-400, which vary in chemical properties and molecular size. We found that transcription was substantially enhanced in the macromolecular crowding solutions; up to 4-fold increase in the mRNA production was detected in the presence of 20% (w/v) of Ficoll-70. In contrast, translation was generally inhibited by the addition of each of the three crowding agents. This might be due to PEG-induced protein precipitation and non-specific binding of translation factors to Ficoll molecules. We further explored a two-stage CFPE in which transcription and translation was carried out under high then low macromolecular crowding conditions, respectively. It produced 2.2-fold higher protein yield than the coupled CFPE control. The macromolecular crowding effects on CFPE were subsequently confirmed by cell-free synthesis of an approximately two-fold larger protein, Firefly luciferase, under macromolecular crowding environments. Conclusions/Significance Three macromolecular crowding agents used in this research had opposite effects on transcription and translation. The results of this study should aid researchers in their choice of macromolecular crowding agents and shows that two-stage CFPE is more efficient than coupled CFPE.
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Jianfeng Xu
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, Arkansas, United States of America
- * E-mail:
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28
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Kovtun O, Mureev S, Jung W, Kubala MH, Johnston W, Alexandrov K. Leishmania cell-free protein expression system. Methods 2011; 55:58-64. [PMID: 21704167 DOI: 10.1016/j.ymeth.2011.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/02/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022] Open
Abstract
Cell-free protein expression is an important tool for a rapid production, engineering and labeling of recombinant proteins. However the complex protocols for preparation of eukaryotic cell-free protein expression systems result in high manufacturing costs and limit their utility. Recently we reported a novel cell-free expression system based on the lysate of a fermentable protozoan Leishmania tarentolae. Herein we describe a protocol for high throughput protein expression using Leishmania cell-free lysate. The protocol combines PCR-based synthesis and engineering of translation templates with a combined transcription-translation system. The protocol is adapted to multiwell plate format and allows translation of large protein libraries. In the presented example we translate in vitro and isolate a nearly complete complement of mammalian Rab GTPases. Further applications and developments of the system are discussed.
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Affiliation(s)
- Oleksiy Kovtun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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29
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Ogawa A, Doi Y, Matsushita N. Improvement of in vitro-transcribed amber suppressor tRNAs toward higher suppression efficiency in wheat germ extract. Org Biomol Chem 2011; 9:8495-503. [DOI: 10.1039/c1ob06351k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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