1
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Sánchez-Costa M, Urigoitia A, Comino N, Arnaiz B, Khatami N, Ruiz-Hernandez R, Diamanti E, Abarrategi A, López-Gallego F. In-Hydrogel Cell-Free Protein Expression System as Biocompatible and Implantable Biomaterial. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15993-16002. [PMID: 38509001 DOI: 10.1021/acsami.4c01388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Biomaterials capable of delivering therapeutic proteins are relevant in biomedicine, yet their manufacturing relies on centralized manufacturing chains that pose challenges to their remote implementation at the point of care. This study explores the viability of confined cell-free protein synthesis within porous hydrogels as biomaterials that dynamically produce and deliver proteins to in vitro and in vivo biological microenvironments. These functional biomaterials have the potential to be assembled as implants at the point of care. To this aim, we first entrap cell-free extracts (CFEs) from Escherichia coli containing the transcription-translation machinery, together with plasmid DNA encoding the super folded green fluorescence protein (sGFP) as a model protein, into hydrogels using various preparation methods. Agarose hydrogels result in the most suitable biomaterials to confine the protein synthesis system, demonstrating efficient sGFP production and diffusion from the core to the surface of the hydrogel. Freeze-drying (FD) of agarose hydrogels still allows for the synthesis and diffusion of sGFP, yielding a more attractive biomaterial for its reconstitution and implementation at the point of care. FD-agarose hydrogels are biocompatible in vitro, allowing for the colonization of cell microenvironments along with cell proliferation. Implantation assays of this biomaterial in a preclinical mouse model proved the feasibility of this protein synthesis approach in an in vivo context and indicated that the physical properties of the biomaterials influence their immune responses. This work introduces a promising avenue for biomaterial fabrication, enabling the in vivo synthesis and targeted delivery of proteins and opening new paths for advanced protein therapeutic approaches based on biocompatible biomaterials.
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Affiliation(s)
| | - Ane Urigoitia
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Natalia Comino
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Blanca Arnaiz
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Neda Khatami
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- Polymat, University of Basque Country UPV/EHU, Donostia/San Sebastián 20018, Gipuzkoa, Spain
| | | | - Eleftheria Diamanti
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Ander Abarrategi
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Spain
| | - Fernando López-Gallego
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Spain
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2
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Wang T, Lu Y. Toward Minimal Transcription-Translation Machinery. ACS Synth Biol 2023; 12:3312-3327. [PMID: 37852206 DOI: 10.1021/acssynbio.3c00324] [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: 10/20/2023]
Abstract
With the advantages of simple genetic composition, low metabolic background, low energy waste, and high genetic stability, genome-reduced strains, as promising functional chassis, have become an intensive direction for constructing potent biosynthesis factories. Herein, an innovative Genome-Reduced strain-based Active Cell-free Easy-to-make-protein (GRACE) system is built as minimal transcription-translation machinery. In this study, two Escherichia coli genome-reduced strains, ΔW3110 and ΔMG1655, with genome reduction of 11.53% and 37.85%, are fused with the cell-free transcription-translation (CFTT) system. The GRACE systems perform better than the corresponding CFTT systems derived from their parental strains in representative valuable applications, such as the expression and solubilization of membrane proteins or protein polymers, biosensing of inorganic or organic molecules based on different principles, and unnatural amino acid embedding. Obviously, the GRACE system has provided a brand-new enabling platform for cell-free transcription-translation basic and applied studies and also would inspire the potential of genome-reduced strains for versatile applications.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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3
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Bains J, Qureshi N, Ceylan B, Wacker A, Schwalbe H. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function. Nucleic Acids Res 2023; 51:e82. [PMID: 37409574 PMCID: PMC10450168 DOI: 10.1093/nar/gkad574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
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Affiliation(s)
- Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
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4
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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Characterization of Phosphorylation Status and Kinase Activity of Src Family Kinases Expressed in Cell-Based and Cell-Free Protein Expression Systems. Biomolecules 2021; 11:biom11101448. [PMID: 34680080 PMCID: PMC8533471 DOI: 10.3390/biom11101448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022] Open
Abstract
The production of heterologous proteins is an important procedure for biologists in basic and applied sciences. A variety of cell-based and cell-free protein expression systems are available to achieve this. The expression system must be selected carefully, especially for target proteins that require post-translational modifications. In this study, human Src family kinases were prepared using six different protein expression systems: 293 human embryonic kidney cells, Escherichia coli, and cell-free expression systems derived from rabbit reticulocytes, wheat germ, insect cells, or Escherichia coli. The phosphorylation status of each kinase was analyzed by Phos-tag SDS-PAGE. The kinase activities were also investigated. In the eukaryotic systems, multiple phosphorylated forms of the expressed kinases were observed. In the rabbit reticulocyte lysate system and 293 cells, differences in phosphorylation status between the wild-type and kinase-dead mutants were observed. Whether the expressed kinase was active depended on the properties of both the kinase and each expression system. In the prokaryotic systems, Src and Hck were expressed in autophosphorylated active forms. Clear differences in post-translational phosphorylation among the protein expression systems were revealed. These results provide useful information for preparing functional proteins regulated by phosphorylation.
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6
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Ge X, Xu J. Macromolecular crowding effects on transcription and translation are regulated by free magnesium ion. Biotechnol Appl Biochem 2019; 67:117-122. [PMID: 31576614 DOI: 10.1002/bab.1827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/28/2019] [Indexed: 12/21/2022]
Abstract
Cell-free metabolic engineering is an emerging and promising alternative platform for the production of fuels and chemicals. In recent years, macromolecular crowding effect, which is an important function in living cells but ignored in cell-free systems, has been transferred to cell-free protein synthesis (CFPS). However, inhibitory effects of crowding agents on CFPS were frequently observed, and the mechanism is unclear. In this study, free Mg2+ was found to be a key factor that can regulate the macromolecular crowding effect on in vitro transcription, in vitro translation, and coupled transcript/translation. Addition of crowding agents (20% of Ficoll-70 or Ficoll-400) enhanced in vitro transcription at an index of free Mg2+ concentration (IFMC) below 2 mM but inhibited the transcription when the IFMC was higher than 2 mM. Similarly, Ficoll-400 enhanced in vitro translation and coupled transcription/translation at a lower IFMC (0.1-2 mM) and inhibited the reactions at higher IFMC (>2 mM). Based on the results, CFPS systems could be further optimized by adjusting the content of crowding agents and the IFMC. Besides, the results also indicate that macromolecular crowding effect is important for maintaining the efficiency of in vivo transcription and translation which occur at a low intracellular IFMC (<1 mM).
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, AR, USA.,Quasar Energy Group, Independence, OH, USA
| | - Jianfeng Xu
- Arkansas Biosciences Institute and College of Agriculture and Technology, Arkansas State University, Jonesboro, AR, USA
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7
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Krinsky N, Kaduri M, Zinger A, Shainsky-Roitman J, Goldfeder M, Benhar I, Hershkovitz D, Schroeder A. Synthetic Cells Synthesize Therapeutic Proteins inside Tumors. Adv Healthc Mater 2018; 7:e1701163. [PMID: 29283226 PMCID: PMC6684359 DOI: 10.1002/adhm.201701163] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/11/2017] [Indexed: 12/14/2022]
Abstract
Synthetic cells, artificial cell-like particles, capable of autonomously synthesizing RNA and proteins based on a DNA template, are emerging platforms for studying cellular functions and for revealing the origins-of-life. Here, it is shown for the first time that artificial lipid-based vesicles, containing the molecular machinery necessary for transcription and translation, can be used to synthesize anticancer proteins inside tumors. The synthetic cells are engineered as stand-alone systems, sourcing nutrients from their biological microenvironment to trigger protein synthesis. When pre-loaded with template DNA, amino acids and energy-supplying molecules, up to 2 × 107 copies of green fluorescent protein are synthesized in each synthetic cell. A variety of proteins, having molecular weights reaching 66 kDa and with diagnostic and therapeutic activities, are synthesized inside the particles. Incubating synthetic cells, encoded to secrete Pseudomonas exotoxin A (PE) with 4T1 breast cancer cells in culture, resulted in killing of most of the malignant cells. In mice bearing 4T1 tumors, histological evaluation of the tumor tissue after a local injection of PE-producing particles indicates robust apoptosis. Synthetic cells are new platforms for synthesizing therapeutic proteins on-demand in diseased tissues.
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Affiliation(s)
- Nitzan Krinsky
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
- The Interdisciplinary Programs for Biotechnology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Kaduri
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Assaf Zinger
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Janna Shainsky-Roitman
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Mor Goldfeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Dov Hershkovitz
- Department of Pathology, Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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8
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Damiati S, Mhanna R, Kodzius R, Ehmoser EK. Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics. Genes (Basel) 2018; 9:E144. [PMID: 29509709 PMCID: PMC5867865 DOI: 10.3390/genes9030144] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rami Mhanna
- Biomedical Engineering Program, The American University of Beirut (AUB), Beirut 1107-2020, Lebanon.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Eva-Kathrin Ehmoser
- Department of Nanobiotechnology, Institute for Synthetic Bioarchitecture, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
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Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits. Methods Mol Biol 2018; 1772:61-93. [PMID: 29754223 DOI: 10.1007/978-1-4939-7795-6_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the past decade, a new generation of cell-free transcription-translation (TXTL) systems has been devised for emerging multidisciplinary applications. The DNA-dependent in vitro protein synthesis technology has been developed to tackle applications in synthetic biology, biological and chemical engineering, as well as quantitative disciplines such as biophysics. In addition to being convenient at the biosafety level, the new TXTL platforms are user-friendly; more affordable; more versatile at the level of transcription, with a TX repertoire covering hundreds of parts; and more powerful, with protein production reaching a few mg/mL in batch and continuous modes. As a consequence, TXTL is rising up as a popular research tool and is used by a growing research community. While TXTL is proving reliable for an increasing number of applications, it is important to gain appropriate TXTL skills, especially for quantitative applications. TXTL has become particularly useful to rapidly prototype genetic devices , from single regulatory elements to elementary circuit motifs . In this chapter, we describe the basic procedures to develop appropriate TXTL practices for the characterization of such genetic parts. We use an all E. coli TXTL system developed in our lab, now commercialized by Arbor Biosciences under the name myTXTL.
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10
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Didovyk A, Tonooka T, Tsimring L, Hasty J. Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression. ACS Synth Biol 2017; 6:2198-2208. [PMID: 28795570 DOI: 10.1021/acssynbio.7b00253] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducible, and a labor- and cost-effective approach for rapid production of bacterial lysates for cell-free gene expression. Using this method, robust and highly active bacterial cell lysates can be produced without specialized equipment at a wide range of scales, making cell-free gene expression easily and broadly accessible. Moreover, live autolysis strain can be freeze-dried directly and subsequently lysed upon rehydration to produce active lysate. We demonstrate the utility of autolysates for synthetic biology by regulating protein production and degradation, implementing quorum sensing, and showing quantitative protection of linear DNA templates by GamS protein. To allow versatile and sensitive β-galactosidase (LacZ) based readout we produce autolysates with no detectable background LacZ activity and use them to produce sensitive mercury(II) biosensors with LacZ-mediated colorimetric and fluorescent outputs. The autolysis approach can facilitate wider adoption of cell-free technology for cell-free gene expression as well as other synthetic biology and biotechnology applications, such as metabolic engineering, natural product biosynthesis, or proteomics.
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Affiliation(s)
- Andriy Didovyk
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Taishi Tonooka
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Lev Tsimring
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Jeff Hasty
- BioCircuits
Institute, University of California San Diego, La Jolla, California 92093, United States
- San
Diego Center for Systems Biology, University of California San Diego, La Jolla, California 92093, United States
- Department
of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Molecular
Biology Section, Division of Biological Science, University of California San Diego, La Jolla, California 92093, United States
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11
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Stano P, Altamura E, Mavelli F. Novel directions in molecular systems design: The case of light-transducing synthetic cells. Commun Integr Biol 2017; 10:e1365993. [PMID: 29260799 PMCID: PMC5731512 DOI: 10.1080/19420889.2017.1365993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022] Open
Abstract
Important progresses have been achieved in the past years in the field of bottom-up synthetic biology, especially aiming at constructing cell-like systems based on lipid vesicles (liposomes) entrapping both biomolecules or synthetic compounds. These "synthetic cells" mimic the behaviour of biological cells but are constituted by a minimal number of components. One key aspect related to this research is the energetic needs of synthetic cells. Up to now, high-energy compounds have been given in order to drive biochemical reactions inside the vesicle lumen. In order to be autonomous, synthetic cells must produce their own biochemical energy from available energy sources. At this aim we started a long-term research program focused on the construction of photoautotrophic synthetic cells, starting with the reconstitution, in active and highly oriented form, of the photosynthetic reaction centre in giant lipid vesicles (Altamura et al., PNAS 2017, 114, 3837-3842). Here we comment this first milestone by showing the synthetic biology context wherein it is developed, the future steps, and the experimental approach that might allow such an achievement.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, Lecce, Italy
| | | | - Fabio Mavelli
- Chemistry Department, University “Aldo Moro,” Bari, Italy
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12
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Del Prete S, Perfetto R, Rossi M, Alasmary FAS, Osman SM, AlOthman Z, Supuran CT, Capasso C. A one-step procedure for immobilising the thermostable carbonic anhydrase (SspCA) on the surface membrane of Escherichia coli. J Enzyme Inhib Med Chem 2017; 32:1120-1128. [PMID: 28791907 PMCID: PMC6010132 DOI: 10.1080/14756366.2017.1355794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The carbonic anhydrase superfamily (CA, EC 4.2.1.1) of metalloenzymes is present in all three domains of life (Eubacteria, Archaea, and Eukarya), being an interesting example of convergent/divergent evolution, with its seven families (α-, β-, γ-, δ-, ζ-, η-, and θ-CAs) described so far. CAs catalyse the simple, but physiologically crucial reaction of carbon dioxide hydration to bicarbonate and protons. Recently, our groups characterised the α-CA from the thermophilic bacterium, Sulfurihydrogenibium yellowstonense finding a very high catalytic activity for the CO2 hydration reaction (kcat = 9.35 × 105 s-1 and kcat/Km = 1.1 × 108 M-1 s-1) which was maintained after heating the enzyme at 80 °C for 3 h. This highly thermostable SspCA was covalently immobilised within polyurethane foam and onto the surface of magnetic Fe3O4 nanoparticles. Here, we describe a one-step procedure for immobilising the thermostable SspCA directly on the surface membrane of Escherichia coli, using the INPN domain of Pseudomonas syringae. This strategy has clear advantages with respect to other methods, which require as the first step the production and the purification of the biocatalyst, and as the second step the immobilisation of the enzyme onto a specific support. Our results demonstrate that thermostable SspCA fused to the INPN domain of P. syringae ice nucleation protein (INP) was correctly expressed on the outer membrane of engineered E. coli cells, affording for an easy approach to design biotechnological applications for this highly effective thermostable catalyst.
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Affiliation(s)
- Sonia Del Prete
- a Dipartimento di Scienze Bio-Agroalimentari, CNR-Istituto di Bioscienze e Biorisorse , CNR , Napoli , Italy.,b Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, and Laboratorio di Chimica Bioinorganica, Polo Scientifico , Università degli Studi di Firenze , Florence , Italy
| | - Rosa Perfetto
- a Dipartimento di Scienze Bio-Agroalimentari, CNR-Istituto di Bioscienze e Biorisorse , CNR , Napoli , Italy
| | - Mosè Rossi
- a Dipartimento di Scienze Bio-Agroalimentari, CNR-Istituto di Bioscienze e Biorisorse , CNR , Napoli , Italy
| | - Fatmah A S Alasmary
- c Department of Chemistry, College of Science , King Saud University , Riyadh , Saudi Arabia
| | - Sameh M Osman
- c Department of Chemistry, College of Science , King Saud University , Riyadh , Saudi Arabia
| | - Zeid AlOthman
- c Department of Chemistry, College of Science , King Saud University , Riyadh , Saudi Arabia
| | - Claudiu T Supuran
- b Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, and Laboratorio di Chimica Bioinorganica, Polo Scientifico , Università degli Studi di Firenze , Florence , Italy
| | - Clemente Capasso
- a Dipartimento di Scienze Bio-Agroalimentari, CNR-Istituto di Bioscienze e Biorisorse , CNR , Napoli , Italy
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13
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Ashkani J, Rees DJG. Selecting an appropriate method for expressing S locus F-box-S2 recombinant protein. ACTA ACUST UNITED AC 2017; 15:41-47. [PMID: 28664149 PMCID: PMC5480281 DOI: 10.1016/j.btre.2017.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/27/2017] [Accepted: 06/15/2017] [Indexed: 11/23/2022]
Abstract
Understanding the molecular basis of self-incompatibility (SI) is essential for commercial production of fruit crops such as Apple. To investigate the molecular interactions in self-incompatibility locus (Slocus), the knowledge of tertiary structures of both male (i.e. S-locus F-box) and female (i.e. SRNase) proteins are necessary. The tertiary structure of male determinant (S locus F-box, SLF/SFB) remains unresolved, which could mainly be due to difficulties associated with its expression in the recombinant expression systems. This study demonstrates an approach for efficient expression of S locus F-box recombinant proteins for future functional and structural studies.
A single locus (S locus) including at least two linked genes (female and male determinants) genetically controls the gametophytic self-incompatibility (GSI) in apple, which has evolved to avoid self-fertilization. There has been extensive work done on the female determinant of self-incompatibility, which has led to the determination of the tertiary structure of S-RNase. However, the tertiary structure of male determinant (S locus F-box, SLF/SFB) remains unresolved, which could mainly be due to difficulties associated with its expression in the recombinant expression systems. In addressing this, we have evaluated several in vivo (prokaryotic and eukaryotic) and in vitro expression systems for their efficiency in the expression of apple SLF2. The most successful expression of SLF2 (1 mg/ml) was achieved in E. coli using the synthesized gene in a high salt culture and applying heat shock before induction of culture. We therefore present an approach for the efficient expression of S locus F-box recombinant proteins for future functional and structural studies.
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Affiliation(s)
- Jahanshah Ashkani
- Biotechnology Department, University of the Western Cape, Robert Sobokwe Road, Bellville, 7535, South Africa.,Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
| | - D J G Rees
- Biotechnology Department, University of the Western Cape, Robert Sobokwe Road, Bellville, 7535, South Africa.,Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
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14
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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15
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Garamella J, Marshall R, Rustad M, Noireaux V. The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology. ACS Synth Biol 2016; 5:344-55. [PMID: 26818434 DOI: 10.1021/acssynbio.5b00296] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report on and provide a detailed characterization of the performance and properties of a recently developed, all Escherichia coli, cell-free transcription and translation system. Gene expression is entirely based on the endogenous translation components and transcription machinery provided by an E. coli cytoplasmic extract, thus expanding the repertoire of regulatory parts to hundreds of elements. We use a powerful metabolism for ATP regeneration to achieve more than 2 mg/mL of protein synthesis in batch mode reactions, and more than 6 mg/mL in semicontinuous mode. While the strength of cell-free expression is increased by a factor of 3 on average, the output signal of simple gene circuits and the synthesis of entire bacteriophages are increased by orders of magnitude compared to previous results. Messenger RNAs and protein degradation, respectively tuned using E. coli MazF interferase and ClpXP AAA+ proteases, are characterized over a much wider range of rates than the first version of the cell-free toolbox. This system is a highly versatile cell-free platform to construct complex biological systems through the execution of DNA programs composed of synthetic and natural bacterial regulatory parts.
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Affiliation(s)
- Jonathan Garamella
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Ryan Marshall
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Mark Rustad
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School
of Physics and Astronomy, University of Minnesota, 115 Union
Street SE, Minneapolis, Minnesota 55455, United States
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16
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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17
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Zieleniecki JL, Nagarajan Y, Waters S, Rongala J, Thompson V, Hrmova M, Köper I. Cell-Free Synthesis of a Functional Membrane Transporter into a Tethered Bilayer Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2445-2449. [PMID: 26910192 DOI: 10.1021/acs.langmuir.5b04059] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Eukaryotic cell-free synthesis was used to incorporate the large and complex multispan plant membrane transporter Bot1 in a functional form into a tethered bilayer lipid membrane. The electrical properties of the protein-functionalized tethered bilayer were measured using electrochemical impedance spectroscopy and revealed a pH-dependent transport of borate ions through the protein. The efficacy of the protein synthesis has been evaluated using immunoblot analysis.
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Affiliation(s)
- Julius L Zieleniecki
- Flinders Centre for Nanoscale Science and Technology School of Chemical and Physical Sciences, Flinders University , Bedford Park, South Australia 5042, Australia
| | - Yagnesh Nagarajan
- Australian Centre for Plant Functional Genomics School of Agriculture, Food, and Wine, University of Adelaide , Glen Osmond, South Australia 5064, Australia
| | - Shane Waters
- Australian Centre for Plant Functional Genomics School of Agriculture, Food, and Wine, University of Adelaide , Glen Osmond, South Australia 5064, Australia
| | - Jay Rongala
- Australian Centre for Plant Functional Genomics School of Agriculture, Food, and Wine, University of Adelaide , Glen Osmond, South Australia 5064, Australia
| | - Vanessa Thompson
- Flinders Centre for Nanoscale Science and Technology School of Chemical and Physical Sciences, Flinders University , Bedford Park, South Australia 5042, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics School of Agriculture, Food, and Wine, University of Adelaide , Glen Osmond, South Australia 5064, Australia
| | - Ingo Köper
- Flinders Centre for Nanoscale Science and Technology School of Chemical and Physical Sciences, Flinders University , Bedford Park, South Australia 5042, Australia
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18
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Ashaari NS, Ramarad S, Khairuddin D, Akhir NAM, Hara Y, Mahadi NM, Mohamed R, Nathan S. Development of repeatable arrays of proteins using immobilized DNA microplate (RAPID-M) technology. BMC Res Notes 2015; 8:669. [PMID: 26563904 PMCID: PMC4642736 DOI: 10.1186/s13104-015-1637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/26/2015] [Indexed: 11/30/2022] Open
Abstract
Background Protein microarrays have enormous
potential as in vitro diagnostic tools stemming from the ability to miniaturize whilst generating maximum evaluation of diagnostically relevant information from minute amounts of sample. In this report, we present a method known as repeatable arrays of proteins using immobilized DNA microplates (RAPID-M) for high-throughput in situ protein microarray fabrication. The RAPID-M technology comprises of cell-free expression using immobilized DNA templates and in situ protein purification onto standard microarray slides. Results To demonstrate proof-of-concept, the repeatable protein arrays developed using our RAPID-M technology utilized green fluorescent protein (GFP) and a bacterial outer membrane protein (OmpA) as the proteins of interest for microarray fabrication. Cell-free expression of OmpA and GFP proteins using beads-immobilized DNA yielded protein bands with the expected molecular sizes of 27 and 30 kDa, respectively. We demonstrate that the beads-immobilized DNA remained stable for at least four cycles of cell-free expression. The OmpA and GFP proteins were still functional after in situ purification on the Ni–NTA microarray slide. Conclusion The RAPID-M platform for protein microarray fabrication of two different representative proteins was successfully developed.
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Affiliation(s)
- Nur Suhanawati Ashaari
- Malaysia Genome Institute, 43000, Bangi, Selangor DE, Malaysia. .,Xynergen Sdn. Bhd., UKM Technology Centre, 43600, Bangi, Selangor DE, Malaysia.
| | - Suganti Ramarad
- Xynergen Sdn. Bhd., UKM Technology Centre, 43600, Bangi, Selangor DE, Malaysia.
| | - Dzulaikha Khairuddin
- Malaysia Genome Institute, 43000, Bangi, Selangor DE, Malaysia. .,Xynergen Sdn. Bhd., UKM Technology Centre, 43600, Bangi, Selangor DE, Malaysia.
| | - Nor Azurah Mat Akhir
- Malaysia Genome Institute, 43000, Bangi, Selangor DE, Malaysia. .,Xynergen Sdn. Bhd., UKM Technology Centre, 43600, Bangi, Selangor DE, Malaysia.
| | - Yuka Hara
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor DE, Malaysia. .,INTI International University, Bandar Baru Nilai, 71800, Nilai, Negeri Sembilan, Malaysia.
| | | | - Rahmah Mohamed
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor DE, Malaysia. .,INTI International University, Bandar Baru Nilai, 71800, Nilai, Negeri Sembilan, Malaysia.
| | - Sheila Nathan
- Malaysia Genome Institute, 43000, Bangi, Selangor DE, Malaysia. .,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor DE, Malaysia.
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19
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Worst EG, Exner MP, De Simone A, Schenkelberger M, Noireaux V, Budisa N, Ott A. Cell-free expression with the toxic amino acid canavanine. Bioorg Med Chem Lett 2015; 25:3658-60. [DOI: 10.1016/j.bmcl.2015.06.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 01/29/2023]
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20
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Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 2015; 86:60-72. [DOI: 10.1016/j.ymeth.2015.05.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
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21
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Jackson K, Kanamori T, Ueda T, Fan ZH. Protein synthesis yield increased 72 times in the cell-free PURE system. Integr Biol (Camb) 2015; 6:781-8. [PMID: 25008400 DOI: 10.1039/c4ib00088a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Compared to cell-based protein expression, cell-free protein synthesis (CFPS) offers several advantages including a greater control over system additives. This control is further enhanced with a CFPS system called the Protein synthesis Using Recombinant Elements (PURE) system, which consists of 108 purified transcriptional and translational elements. With the PURE system, all elements are known, nuclease and protease activities are reduced, and the concentration of each element can be optimized for maximal protein expression. However, protein expression yield with this system is relatively low due to the consumption of nutrients and energy molecules as well as the accumulation of inhibitory byproducts in the batch format. To enhance protein expression with the PURE system, we developed a feeding solution that was optimized using a miniaturized fluid array device (μFAD) in a continuous-exchange cell-free (CECF) format. The device enabled (1) continuous supply of energy/nutrient molecules from the feeding solution to the reaction solution where protein synthesis occurred, and (2) simultaneous removal of inhibitory expression byproducts from the reaction solution to the feeding solution. Consequently, the synthesis yield of green fluorescent protein (GFP) increased 72.5-fold in comparison with the same reaction in the conventional batch format.
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Affiliation(s)
- Kirsten Jackson
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611, USA
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22
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
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Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
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24
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Lian Q, Cao H, Wang F. The Cost-Efficiency Realization in the Escherichia coli-Based Cell-Free Protein Synthesis Systems. Appl Biochem Biotechnol 2014; 174:2351-67. [DOI: 10.1007/s12010-014-1143-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/06/2014] [Indexed: 01/08/2023]
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25
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Jackson K, Fan ZH. Cell-Free Protein Synthesis in Miniaturized Array Devices and Effects of Device Orientation. ACTA ACUST UNITED AC 2014; 19:366-74. [DOI: 10.1177/2211068213501497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Indexed: 11/17/2022]
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26
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Tokmakov AA. Identification of multiple physicochemical and structural properties associated with soluble expression of eukaryotic proteins in cell-free bacterial extracts. Front Microbiol 2014; 5:295. [PMID: 24999341 PMCID: PMC4064534 DOI: 10.3389/fmicb.2014.00295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022] Open
Abstract
Bacterial extracts are widely used to synthesize recombinant proteins. Vast data volumes have been accumulated in cell-free expression databases, covering a whole range of existing proteins. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with protein solubility and aggregation. In the present paper, an approach to identify the multiple physicochemical and structural properties of amino acid sequences associated with soluble expression of eukaryotic proteins in cell-free bacterial extracts is presented. The method includes: (1) categorical assessment of expression data; (2) calculation and prediction of multiple properties of expressed sequences; (3) correlation of the individual properties with the expression scores; and (4) evaluation of statistical significance of the observed correlations. Using this method, a number of significant correlations between calculated and predicted properties of amino acid sequences and their propensity for soluble cell-free expression have been revealed.
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27
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Richter C, Bickel F, Osberghaus A, Hubbuch J. High-throughput characterization of an insect cell-free expression. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Carolin Richter
- Karlsruhe Institute of Technology; Institute of Process Engineering in Life Sciences; Section IV: Biomolecular Separation Engineering; Karlsruhe Germany
| | - Fabian Bickel
- Biberach University of Applied Science; Institute of Applied Science; Biberach/Riss Germany
| | - Anna Osberghaus
- Karlsruhe Institute of Technology; Institute of Process Engineering in Life Sciences; Section IV: Biomolecular Separation Engineering; Karlsruhe Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology; Institute of Process Engineering in Life Sciences; Section IV: Biomolecular Separation Engineering; Karlsruhe Germany
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28
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Coutable A, Thibault C, Chalmeau J, François JM, Vieu C, Noireaux V, Trévisiol E. Preparation of tethered-lipid bilayers on gold surfaces for the incorporation of integral membrane proteins synthesized by cell-free expression. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3132-3141. [PMID: 24568716 DOI: 10.1021/la5004758] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
There is an increasing interest to express and study membrane proteins in vitro. New techniques to produce and insert functional membrane proteins into planar lipid bilayers have to be developed. In this work, we produce a tethered lipid bilayer membrane (tBLM) to provide sufficient space for the incorporation of the integral membrane protein (IMP) Aquaporin Z (AqpZ) between the tBLM and the surface of the sensor. We use a gold (Au)-coated sensor surface compatible with mechanical sensing using a quartz crystal microbalance with dissipation monitoring (QCM-D) or optical sensing using the surface plasmon resonance (SPR) method. tBLM is produced by vesicle fusion onto a thin gold film, using phospholipid-polyethylene glycol (PEG) as a spacer. Lipid vesicles are composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-poly(ethyleneglycol)-2000-N-[3-(2-pyridyldithio)propionate], so-called DSPE-PEG-PDP, at different molar ratios (respectively, 99.5/0.5, 97.5/2.5, and 95/5 mol %), and tBLM formation is characterized using QCM-D, SPR, and atomic force technology (AFM). We demonstrate that tBLM can be produced on the gold surface after rupture of the vesicles using an α helical (AH) peptide, derived from hepatitis C virus NS5A protein, to assist the fusion process. A cell-free expression system producing the E. coli integral membrane protein Aquaporin Z (AqpZ) is directly incubated onto the tBLMs for expression and insertion of the IMP at the upper side of tBLMs. The incorporation of AqpZ into bilayers is monitored by QCM-D and compared to a control experiment (without plasmid in the cell-free expression system). We demonstrate that an IMP such as AqpZ, produced by a cell-free expression system without any protein purification, can be incorporated into an engineered tBLM preassembled at the surface of a gold-coated sensor.
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Affiliation(s)
- Angélique Coutable
- Université de Toulouse , INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
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29
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Richter C, Konstantinidis K, Asen I, Kneusel R, Hubbuch J. Cell-free expression of recombinant antigens ofBorrelia burgdorferiand microarray-based multiplex detection using different patient sera. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Carolin Richter
- DIARECT AG; Freiburg Germany
- Karlsruhe Institute of Technology; Institute of Process Engineering in Life Sciences; Section IV: Biomolecular Separation Engineering; Karlsruhe Germany
| | | | | | - Richard Kneusel
- DIARECT AG; Freiburg Germany
- BadenBioTec GmbH; Freiburg Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology; Institute of Process Engineering in Life Sciences; Section IV: Biomolecular Separation Engineering; Karlsruhe Germany
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30
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Abstract
The lack of high-throughput approaches for expression and screening of large enzyme libraries remains a major bottleneck for current enzyme engineering efforts. To address this need, we have developed a high-throughput, fluorescence-based approach for rapid one-pot, microscale expression, and screening of industrial enzymes. In this chapter, we present the protocol for integration of cell-free protein expression with activity screening of enzymes in two formats: (1) a 96-well plate format and (2) a microscale-array format. Our one-pot method is ideally suited for rapid, first pass screening of enzymes and can also be used to perform detailed mechanistic analysis such as measurement of kinetics, determination of optimum temperature, and to study enzyme inhibition.
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32
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Hirose S, Noguchi T. ESPRESSO: a system for estimating protein expression and solubility in protein expression systems. Proteomics 2013; 13:1444-56. [PMID: 23436767 DOI: 10.1002/pmic.201200175] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 01/27/2013] [Accepted: 02/06/2013] [Indexed: 11/11/2022]
Abstract
Recombinant protein technology is essential for conducting protein science and using proteins as materials in pharmaceutical or industrial applications. Although obtaining soluble proteins is still a major experimental obstacle, knowledge about protein expression/solubility under standard conditions may increase the efficiency and reduce the cost of proteomics studies. In this study, we present a computational approach to estimate the probability of protein expression and solubility for two different protein expression systems: in vivo Escherichia coli and wheat germ cell-free, from only the sequence information. It implements two kinds of methods: a sequence/predicted structural property-based method that uses both the sequence and predicted structural features, and a sequence pattern-based method that utilizes the occurrence frequencies of sequence patterns. In the benchmark test, the proposed methods obtained F-scores of around 70%, and outperformed publicly available servers. Applying the proposed methods to genomic data revealed that proteins associated with translation or transcription have a strong tendency to be expressed as soluble proteins by the in vivo E. coli expression system. The sequence pattern-based method also has the potential to indicate a candidate region for modification, to increase protein solubility. All methods are available for free at the ESPRESSO server (http://mbs.cbrc.jp/ESPRESSO).
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Affiliation(s)
- Shuichi Hirose
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
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33
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Lanzi A, Fehres CM, de Gruijl TD, van Kooyk Y, Mastrobattista E. Effects of antigen-expressing immunostimulatory liposomes on chemotaxis and maturation of dendritic cells in vitro and in human skin explants. Pharm Res 2013; 31:516-26. [PMID: 24072262 DOI: 10.1007/s11095-013-1179-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/09/2013] [Indexed: 12/15/2022]
Abstract
PURPOSE Antigen-Expressing Immunostimulatory Liposomes (AnExILs) represent a novel DNA vaccination platform based on the production of protein antigens from DNA templates inside liposomes mediated by an in vitro transcription and translation (IVTT) mix. The aim of this study was to analyze the effects of AnExILs on different dendritic cells (DCs) models and to better understand the role of the different components of this formulation on its adjuvanticity. METHODS The effect of β-galactosidase-expressing AnExILs on maturation and particle uptake by murine DC cell line, fresh human monocyte-derived DCs or human dermal DCs in skin explants was investigated and compared to the effects of either plain liposomes or IVTT mix alone. RESULTS AnExILs induced efficient DC chemotaxis and promoted up-regulation of maturation markers on murine DCs, due to the presence of IVTT in the formulation. Furthermore, the amount of active βGal associated with DCs was higher for AnExILs than for free βGal expressed in IVTT or βGal encapsulated into non-adjuvanted liposomes. Most interestingly, the same trend was observed with human DCs. CONCLUSIONS Both IVTT mix and liposomal vehicles were shown to be key components of the AnExIL formulation responsible for its adjuvanticity. AnExILs combine antigen production, adjuvanticity and delivery in one system, and can efficiently activate both murine and human DCs.
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Affiliation(s)
- Anastasia Lanzi
- Department of PharmaceuticsUtrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG, Utrecht, The Netherlands
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34
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Role of messenger RNA–ribosome complex in complementary DNA display. Anal Biochem 2013; 438:97-103. [DOI: 10.1016/j.ab.2013.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 11/20/2022]
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35
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Kwon YC, Oh IS, Lee N, Lee KH, Yoon YJ, Lee EY, Kim BG, Kim DM. Integrating cell-free biosyntheses of heme prosthetic group and apoenzyme for the synthesis of functional P450 monooxygenase. Biotechnol Bioeng 2012; 110:1193-200. [DOI: 10.1002/bit.24785] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 11/07/2022]
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36
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Enhanced in vitro translation at reduced temperatures using a cold-shock RNA motif. Biotechnol Lett 2012; 35:389-95. [DOI: 10.1007/s10529-012-1091-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
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37
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Ebersbach H, Geisse S. Antigen generation and display in therapeutic antibody drug discovery -- a neglected but critical player. Biotechnol J 2012; 7:1433-43. [PMID: 23139179 DOI: 10.1002/biot.201200066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/26/2012] [Accepted: 09/25/2012] [Indexed: 01/17/2023]
Abstract
Disease intervention by targeting a critical pathway molecule through a blocking antibody or interference by therapeutic proteins is currently en vogue. Generation of blocking antibodies or therapeutic proteins inevitably requires the production of recombinant proteins or cell-based immunogens. Thus, one could call the antigen molecule the neglected player in antibody drug discovery. The variety of methods available for making recombinant proteins or recombinant cell lines that present the target on the cell surface is extensive. These need to be addressed in conjunction with biochemical and biophysical quality criteria and the experimental application intended. Fundamentally, successful production and isolation of monoclonal antibodies requires optimized antigen preparation and presentation to the immune host. This review summarizes the most important aspects of antigen generation and display, enabling logical decision making to give rise to potent high-affinity antibodies.
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Affiliation(s)
- Hilmar Ebersbach
- NBC/NT, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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38
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Tokmakov AA, Kurotani A, Takagi T, Toyama M, Shirouzu M, Fukami Y, Yokoyama S. Multiple post-translational modifications affect heterologous protein synthesis. J Biol Chem 2012; 287:27106-16. [PMID: 22674579 DOI: 10.1074/jbc.m112.366351] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Post-translational modifications (PTMs) are required for proper folding of many proteins. The low capacity for PTMs hinders the production of heterologous proteins in the widely used prokaryotic systems of protein synthesis. Until now, a systematic and comprehensive study concerning the specific effects of individual PTMs on heterologous protein synthesis has not been presented. To address this issue, we expressed 1488 human proteins and their domains in a bacterial cell-free system, and we examined the correlation of the expression yields with the presence of multiple PTM sites bioinformatically predicted in these proteins. This approach revealed a number of previously unknown statistically significant correlations. Prediction of some PTMs, such as myristoylation, glycosylation, palmitoylation, and disulfide bond formation, was found to significantly worsen protein amenability to soluble expression. The presence of other PTMs, such as aspartyl hydroxylation, C-terminal amidation, and Tyr sulfation, did not correlate with the yield of heterologous protein expression. Surprisingly, the predicted presence of several PTMs, such as phosphorylation, ubiquitination, SUMOylation, and prenylation, was associated with the increased production of properly folded soluble proteins. The plausible rationales for the existence of the observed correlations are presented. Our findings suggest that identification of potential PTMs in polypeptide sequences can be of practical use for predicting expression success and optimizing heterologous protein synthesis. In sum, this study provides the most compelling evidence so far for the role of multiple PTMs in the stability and solubility of heterologously expressed recombinant proteins.
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Affiliation(s)
- Alexander A Tokmakov
- RIKEN Systems and Structural Biology Center, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
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39
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Freischmidt A, Liss M, Wagner R, Kalbitzer HR, Horn G. RNA secondary structure and in vitro translation efficiency. Protein Expr Purif 2012; 82:26-31. [DOI: 10.1016/j.pep.2011.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 01/01/2023]
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40
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Diz AP, Martínez-Fernández M, Rolán-Alvarez E. Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 2012; 21:1060-80. [PMID: 22268916 DOI: 10.1111/j.1365-294x.2011.05426.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
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Affiliation(s)
- Angel P Diz
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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41
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Ge X, Xu J. Cell-free protein synthesis as a promising expression system for recombinant proteins. Methods Mol Biol 2012; 824:565-578. [PMID: 22160920 DOI: 10.1007/978-1-61779-433-9_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cell-free protein synthesis (CFPS) has major advantages over traditional cell-based methods in the capability of high-throughput protein synthesis and special protein production. During recent decades, CFPS has become an alternative protein production platform for both fundamental and applied purposes. Using Renilla luciferase as model protein, we describe a typical process of CFPS in wheat germ extract system, including wheat germ extract preparation, expression vector construction, in vitro protein synthesis (transcription/translation), and target protein assay.
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Affiliation(s)
- Xumeng Ge
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
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42
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Abstract
Although cell-free expression is a relative newcomer to the biochemical toolbox, it has already been reviewed extensively, even in the more specialized cases such as membrane protein expression, nanolipoprotein particles, and applications to crystallography and nuclear magnetic resonance (NMR). Solid-state NMR is also a newcomer to the structural biology toolbox, with its own specificities in terms of sample preparation. Cell-free expression and solid-state NMR are a promising combination that has already proven useful for the structural study of membrane proteins in their native environment, the hydrated lipid bilayer. We describe below several protocols for preparing MscL, a mechanosensitive membrane channel, using cell-free expression destined for a solid-state NMR study. These protocols are flexible and can easily be applied to other membrane proteins, with minor adjustments.
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Affiliation(s)
- Alaa Abdine
- CNRS and Université Paris Diderot, IBPC, Paris, France
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43
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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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44
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Assembling linear DNA templates for in vitro transcription and translation. Methods Mol Biol 2011. [PMID: 22130984 DOI: 10.1007/978-1-61779-424-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cell-free expression systems provide straightforward access from genes to the corresponding proteins, involving fewer handling steps than in vivo procedures. A quick procedure to assemble a gene of interest into a linear DNA template together with 3'- and 5'-untranslated regions using a coupled uracil-excision-ligation strategy based on USER Enzyme and T4 DNA ligase. This methodology will be useful for repeated cycles of expression and in vitro selection, in which gene libraries are repeatedly assembled and their products and templates regenerated.
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45
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Cardoso FC, Roddick JS, Groves P, Doolan DL. Evaluation of approaches to identify the targets of cellular immunity on a proteome-wide scale. PLoS One 2011; 6:e27666. [PMID: 22096610 PMCID: PMC3214079 DOI: 10.1371/journal.pone.0027666] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/21/2011] [Indexed: 11/19/2022] Open
Abstract
Background Vaccine development against malaria and other complex diseases remains a challenge for the scientific community. The recent elucidation of the genome, proteome and transcriptome of many of these complex pathogens provides the basis for rational vaccine design by identifying, on a proteome-wide scale, novel target antigens that are recognized by T cells and antibodies from exposed individuals. However, there is currently no algorithm to effectively identify important target antigens from genome sequence data; this is especially challenging for T cell targets. Furthermore, for some of these pathogens, such as Plasmodium, protein expression using conventional platforms has been problematic but cell-free in vitro transcription translation (IVTT) strategies have recently proved successful. Herein, we report a novel approach for proteome-wide scale identification of the antigenic targets of T cell responses using IVTT products. Principal Findings We conducted a series of in vitro and in vivo experiments using IVTT proteins either unpurified, absorbed to carboxylated polybeads, or affinity purified through nickel resin or magnetic beads. In vitro studies in humans using CMV, EBV, and Influenza A virus proteins showed antigen-specific cytokine production in ELIspot and Cytometric Bead Array assays with cells stimulated with purified or unpurified IVTT antigens. In vitro and in vivo studies in mice immunized with the Plasmodium yoelii circumsporozoite DNA vaccine with or without IVTT protein boost showed antigen-specific cytokine production using purified IVTT antigens only. Overall, the nickel resin method of IVTT antigen purification proved optimal in both human and murine systems. Conclusions This work provides proof of concept for the potential of high-throughput approaches to identify T cell targets of complex parasitic, viral or bacterial pathogens from genomic sequence data, for rational vaccine development against emerging and re-emerging diseases that pose a threat to public health.
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Affiliation(s)
| | - Joanne S. Roddick
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Penny Groves
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Denise L. Doolan
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- * E-mail:
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46
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Chromophore maturation and fluorescence fluctuation spectroscopy of fluorescent proteins in a cell-free expression system. Anal Biochem 2011; 421:291-8. [PMID: 22093611 DOI: 10.1016/j.ab.2011.10.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 10/15/2011] [Accepted: 10/23/2011] [Indexed: 11/21/2022]
Abstract
Cell-free synthesis, a method for the rapid expression of proteins, is increasingly used to study interactions of complex biological systems. GFP and its variants have become indispensable for fluorescence studies in live cells and are equally attractive as reporters for cell-free systems. This work investigates the use of fluorescence fluctuation spectroscopy (FFS) as a tool for quantitative analysis of protein interactions in cell-free expression systems. We also explore chromophore maturation of fluorescent proteins, which is of crucial importance for fluorescence studies. A droplet sample protocol was developed that ensured sufficient oxygenation for chromophore maturation and ease of manipulation for titration studies. The kinetics of chromophore maturation of EGFP, EYFP, and mCherry were analyzed as a function of temperature. A strong increase in the rate from room temperature to 37°C was observed. We further demonstrate that all EGFP proteins fully mature in the cell-free solution and that brightness is a robust parameter specifying stoichiometry. Finally, FFS is applied to study the stoichiometry of the nuclear transport factor 2 in a cell-free system over a broad concentration range. We conclude that combining cell-free expression and FFS provides a powerful technique for quick, quantitative study of chromophore maturation and protein-protein interaction.
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47
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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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48
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Babel I, Barderas R, Peláez-García A, Casal JI. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen. BMC Biotechnol 2011; 11:61. [PMID: 21635725 PMCID: PMC3125328 DOI: 10.1186/1472-6750-11-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 06/02/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. RESULTS Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. CONCLUSION This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production.
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Affiliation(s)
- Ingrid Babel
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rodrigo Barderas
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Alberto Peláez-García
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - J Ignacio Casal
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
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49
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Hirose S, Kawamura Y, Yokota K, Kuroita T, Natsume T, Komiya K, Tsutsumi T, Suwa Y, Isogai T, Goshima N, Noguchi T. Statistical analysis of features associated with protein expression/solubility in an in vivo Escherichia coli expression system and a wheat germ cell-free expression system. ACTA ACUST UNITED AC 2011; 150:73-81. [DOI: 10.1093/jb/mvr042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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50
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Noireaux V, Maeda YT, Libchaber A. Development of an artificial cell, from self-organization to computation and self-reproduction. Proc Natl Acad Sci U S A 2011; 108:3473-80. [PMID: 21317359 PMCID: PMC3048108 DOI: 10.1073/pnas.1017075108] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This article describes the state and the development of an artificial cell project. We discuss the experimental constraints to synthesize the most elementary cell-sized compartment that can self-reproduce using synthetic genetic information. The original idea was to program a phospholipid vesicle with DNA. Based on this idea, it was shown that in vitro gene expression could be carried out inside cell-sized synthetic vesicles. It was also shown that a couple of genes could be expressed for a few days inside the vesicles once the exchanges of nutrients with the outside environment were adequately introduced. The development of a cell-free transcription/translation toolbox allows the expression of a large number of genes with multiple transcription factors. As a result, the development of a synthetic DNA program is becoming one of the main hurdles. We discuss the various possibilities to enrich and to replicate this program. Defining a program for self-reproduction remains a difficult question as nongenetic processes, such as molecular self-organization, play an essential and complementary role. The synthesis of a stable compartment with an active interface, one of the critical bottlenecks in the synthesis of artificial cell, depends on the properties of phospholipid membranes. The problem of a self-replicating artificial cell is a long-lasting goal that might imply evolution experiments.
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Affiliation(s)
- Vincent Noireaux
- University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455; and
| | - Yusuke T. Maeda
- The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Albert Libchaber
- The Rockefeller University, 1230 York Avenue, New York, NY 10021
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