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Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 2024; 7:1005. [PMID: 39152195 DOI: 10.1038/s42003-024-06690-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ziane Izri
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Oleg Dmytrenko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Patrick Fischer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Chase Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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Levitskaya Z, Ser Z, Koh H, Mei WS, Chee S, Sobota RM, Ghadessy JF. Engineering cell-free systems by chemoproteomic-assisted phenotypic screening. RSC Chem Biol 2024; 5:372-385. [PMID: 38576719 PMCID: PMC10989505 DOI: 10.1039/d4cb00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/16/2024] [Indexed: 04/06/2024] Open
Abstract
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.
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Affiliation(s)
- Zarina Levitskaya
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Zheng Ser
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Hiromi Koh
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Wang Shi Mei
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Sharon Chee
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Radoslaw Mikolaj Sobota
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - John F Ghadessy
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
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3
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Powers J, Jang Y. Advancing Biomimetic Functions of Synthetic Cells through Compartmentalized Cell-Free Protein Synthesis. Biomacromolecules 2023; 24:5539-5550. [PMID: 37962115 DOI: 10.1021/acs.biomac.3c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Synthetic cells are artificial constructs that mimic the structures and functions of living cells. They are attractive for studying diverse biochemical processes and elucidating the origins of life. While creating a living synthetic cell remains a grand challenge, researchers have successfully synthesized hundreds of unique synthetic cell platforms. One promising approach to developing more sophisticated synthetic cells is to integrate cell-free protein synthesis (CFPS) mechanisms into vesicle platforms. This makes it possible to create synthetic cells with complex biomimetic functions such as genetic circuits, autonomous membrane modifications, sensing and communication, and artificial organelles. This Review explores recent advances in the use of CFPS to impart advanced biomimetic structures and functions to bottom-up synthetic cell platforms. We also discuss the potential applications of synthetic cells in biomedicine as well as the future directions of synthetic cell research.
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Affiliation(s)
- Jackson Powers
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, United States
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4
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Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
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Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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5
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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6
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Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
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Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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7
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Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
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Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
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8
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Peruzzi JA, Galvez NR, Kamat NP. Engineering transmembrane signal transduction in synthetic membranes using two-component systems. Proc Natl Acad Sci U S A 2023; 120:e2218610120. [PMID: 37126679 PMCID: PMC10175788 DOI: 10.1073/pnas.2218610120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023] Open
Abstract
Cells use signal transduction across their membranes to sense and respond to a wide array of chemical and physical signals. Creating synthetic systems which can harness cellular signaling modalities promises to provide a powerful platform for biosensing and therapeutic applications. As a first step toward this goal, we investigated how bacterial two-component systems (TCSs) can be leveraged to enable transmembrane-signaling with synthetic membranes. Specifically, we demonstrate that a bacterial two-component nitrate-sensing system (NarX-NarL) can be reproduced outside of a cell using synthetic membranes and cell-free protein expression systems. We find that performance and sensitivity of the TCS can be tuned by altering the biophysical properties of the membrane in which the histidine kinase (NarX) is integrated. Through protein engineering efforts, we modify the sensing domain of NarX to generate sensors capable of detecting an array of ligands. Finally, we demonstrate that these systems can sense ligands in relevant sample environments. By leveraging membrane and protein design, this work helps reveal how transmembrane sensing can be recapitulated outside of the cell, adding to the arsenal of deployable cell-free systems primed for real world biosensing.
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Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL60208
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
| | - Nina R. Galvez
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
| | - Neha P. Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL60208
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9
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Tang Y, Ma S, Lin S, Wu Y, Chen S, Liu G, Ma L, Wang Z, Jiang L, Wang Y. Cell-free protein synthesis of CD1E and B2M protein and in vitro interaction. Protein Expr Purif 2023; 203:106209. [PMID: 36460227 DOI: 10.1016/j.pep.2022.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022]
Abstract
CD1E, one of the most important glycolipid antigens on T cell membranes, is required for glycolipid antigen presentation on the cell surface. Cell-based recombinant expression systems have many limitations for synthesizing transmembrane proteins such as CD1E, including low protein yields and miss folding. To overcome these challenges, here we successfully synthesized high-quality soluble CD1E using an E.coli cell-free protein synthesis system (CFPS) with the aid of detergent. Following purification by Ni2+ affinity chromatography, we were able to obtain CD1E with ≥90% purity. Furthermore, we used the string website to predict the protein interaction network of CD1E and identified a potential binding partner━B2M. Similarly, we synthesized soluble B2M in the E.coli CFPS. Finally, we verified the interaction between CD1E and B2M by using Surface Plasmon Resonance (SPR). Taken together, the methods described here provide an alternative way to obtain active transmembrane protein and may facilitate future structural and functional studies on CD1E.
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Affiliation(s)
- Yajie Tang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Shengming Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Sen Lin
- Anyang Kindstar Global Medical Laboratory LTD, Anyang, Henan province, 455000, China
| | - Yinrong Wu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Siyang Chen
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Gang Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Lisong Ma
- State Key Laboratory of North China Crop Improvement and RegμLation, College of Horticulture, Hebei Agricultural University, Baoding, 071001, China
| | - Zaihua Wang
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lele Jiang
- Surgical Diagnostics Pty Ltd, Roseville, Sydney, 2069, Australia.
| | - Yao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China.
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10
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Clénet D, Clavier L, Strobbe B, Le Bon C, Zoonens M, Saulnier A. Full-length G glycoprotein directly extracted from rabies virus with detergent and then stabilized by amphipols in liquid and freeze-dried forms. Biotechnol Bioeng 2021; 118:4317-4330. [PMID: 34297405 PMCID: PMC9291542 DOI: 10.1002/bit.27900] [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: 07/13/2020] [Revised: 06/22/2021] [Accepted: 07/09/2021] [Indexed: 11/11/2022]
Abstract
Pathogen surface antigens are at the forefront of the viral strategy when invading host organisms. These antigens, including membrane proteins (MPs), are broadly targeted by the host immune response. Obtaining these MPs in a soluble and stable form constitutes a real challenge, regardless of the application purposes (e.g. quantification/characterization assays, diagnosis, and preventive and curative strategies). A rapid process to obtain a native-like antigen by solubilization of a full-length MP directly from a pathogen is reported herein. Rabies virus (RABV) was used as a model for this demonstration and its full-length G glycoprotein (RABV-G) was stabilized with amphipathic polymers, named amphipols (APols). The stability of RABV-G trapped in APol A8-35 (RABV-G/A8-35) was evaluated under different stress conditions (temperature, agitation, and light exposure). RABV-G/A8-35 in liquid form exhibited higher unfolding temperature (+6°C) than in detergent and was demonstrated to be antigenically stable over 1 month at 5°C and 25°C. Kinetic modeling of antigenicity data predicted antigenic stability of RABV-G/A8-35 in a solution of up to 1 year at 5°C. The RABV-G/A8-35 complex formulated in an optimized buffer composition and subsequently freeze-dried displayed long-term stability for 2-years at 5, 25, and 37°C. This study reports for the first time that a natural full-length MP extracted from a virus, complexed to APols and subsequently freeze-dried, displayed long-term antigenic stability, without requiring storage under refrigerated conditions.
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Affiliation(s)
- Didier Clénet
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Léna Clavier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Benoît Strobbe
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Manuela Zoonens
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Aure Saulnier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France.,Department of Analytical Sciences, Sanofi Pasteur, Marcy l'Etoile, France
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11
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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12
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Hershewe JM, Warfel KF, Iyer SM, Peruzzi JA, Sullivan CJ, Roth EW, DeLisa MP, Kamat NP, Jewett MC. Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles. Nat Commun 2021; 12:2363. [PMID: 33888690 PMCID: PMC8062659 DOI: 10.1038/s41467-021-22329-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Cell-free gene expression (CFE) systems from crude cellular extracts have attracted much attention for biomanufacturing and synthetic biology. However, activating membrane-dependent functionality of cell-derived vesicles in bacterial CFE systems has been limited. Here, we address this limitation by characterizing native membrane vesicles in Escherichia coli-based CFE extracts and describing methods to enrich vesicles with heterologous, membrane-bound machinery. As a model, we focus on bacterial glycoengineering. We first use multiple, orthogonal techniques to characterize vesicles and show how extract processing methods can be used to increase concentrations of membrane vesicles in CFE systems. Then, we show that extracts enriched in vesicle number also display enhanced concentrations of heterologous membrane protein cargo. Finally, we apply our methods to enrich membrane-bound oligosaccharyltransferases and lipid-linked oligosaccharides for improving cell-free N-linked and O-linked glycoprotein synthesis. We anticipate that these methods will facilitate on-demand glycoprotein production and enable new CFE systems with membrane-associated activities.
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Affiliation(s)
- Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Shaelyn M Iyer
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
| | - Claretta J Sullivan
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization and Experimentation (NUANCE) Center, Tech Institute A/B Wing A173, Evanston, IL, 60208, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
- Biomedical and Biological Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Neha P Kamat
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Technological Institute E310, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Technological Institute E136, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
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13
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Koo J, Yang J, Park H. Cell-free Systems: Recent Advances and Future Outlook. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Kightlinger W, Warfel KF, DeLisa MP, Jewett MC. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synth Biol 2020; 9:1534-1562. [PMID: 32526139 PMCID: PMC7372563 DOI: 10.1021/acssynbio.0c00210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Protein glycosylation, the attachment of sugars to amino acid side chains, can endow proteins with a wide variety of properties of great interest to the engineering biology community. However, natural glycosylation systems are limited in the diversity of glycoproteins they can synthesize, the scale at which they can be harnessed for biotechnology, and the homogeneity of glycoprotein structures they can produce. Here we provide an overview of the emerging field of synthetic glycobiology, the application of synthetic biology tools and design principles to better understand and engineer glycosylation. Specifically, we focus on how the biosynthetic and analytical tools of synthetic biology have been used to redesign glycosylation systems to obtain defined glycosylation structures on proteins for diverse applications in medicine, materials, and diagnostics. We review the key biological parts available to synthetic biologists interested in engineering glycoproteins to solve compelling problems in glycoscience, describe recent efforts to construct synthetic glycoprotein synthesis systems, and outline exemplary applications as well as new opportunities in this emerging space.
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Affiliation(s)
- Weston Kightlinger
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, 123 Wing Drive, Ithaca, New York 14853, United States
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, New York 14853, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
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15
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McNerney MP, Piorino F, Michel CL, Styczynski MP. Active Analyte Import Improves the Dynamic Range and Sensitivity of a Vitamin B 12 Biosensor. ACS Synth Biol 2020; 9:402-411. [PMID: 31977200 DOI: 10.1021/acssynbio.9b00429] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cell-free systems provide a versatile platform for the development of low-cost, easy-to-use sensors for diverse analytes. However, sensor affinity dictates response sensitivity, and improving binding affinity can be challenging. Here, we describe efforts to address this problem while developing a biosensor for vitamin B12, a critical micronutrient. We first use a B12-responsive transcription factor to enable B12-dependent output in a cell-free reaction, but the resulting sensor responds to B12 far above clinically relevant concentrations. Surprisingly, when expressed in cells, the same sensor mediates a much more sensitive response to B12. The sensitivity difference is partly due to regulated import that accumulates cytoplasmic B12. Overexpression of importers further improves sensitivity, demonstrating an inherent advantage of whole-cell sensors. The resulting cells can respond to B12 in serum, can be lyophilized, and are functional in a minimal-equipment environment, showing the potential utility of whole-cell sensors as sensitive, field-deployable diagnostics.
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Affiliation(s)
- Monica P. McNerney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Fernanda Piorino
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Cirstyn L. Michel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Mark P. Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
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16
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Escherichia coli Extract-Based Cell-Free Expression System as an Alternative for Difficult-to-Obtain Protein Biosynthesis. Int J Mol Sci 2020; 21:ijms21030928. [PMID: 32023820 PMCID: PMC7037961 DOI: 10.3390/ijms21030928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Before utilization in biomedical diagnosis, therapeutic treatment, and biotechnology, the diverse variety of peptides and proteins must be preliminarily purified and thoroughly characterized. The recombinant DNA technology and heterologous protein expression have helped simplify the isolation of targeted polypeptides at high purity and their structure-function examinations. Recombinant protein expression in Escherichia coli, the most-established heterologous host organism, has been widely used to produce proteins of commercial and fundamental research interests. Nonetheless, many peptides/proteins are still difficult to express due to their ability to slow down cell growth or disrupt cellular metabolism. Besides, special modifications are often required for proper folding and activity of targeted proteins. The cell-free (CF) or in vitro recombinant protein synthesis system enables the production of such difficult-to-obtain molecules since it is possible to adjust reaction medium and there is no need to support cellular metabolism and viability. Here, we describe E. coli-based CF systems, the optimization steps done toward the development of highly productive and cost-effective CF methodology, and the modification of an in vitro approach required for difficult-to-obtain protein production.
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17
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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18
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Khambhati K, Bhattacharjee G, Gohil N, Braddick D, Kulkarni V, Singh V. Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems. Front Bioeng Biotechnol 2019; 7:248. [PMID: 31681738 PMCID: PMC6797904 DOI: 10.3389/fbioe.2019.00248] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Cell-free protein synthesis (CFPS) system is a simple, rapid, and sensitive tool that is devoid of membrane-bound barriers, yet contains all the mandatory substrates, biomolecules, and machineries required for the synthesis of the desired proteins. It has the potential to overcome loopholes in the current in vivo production systems and is a promising tool in both basic and applied scientific research. It facilitates a simplified organization of desired experiments with a variety of reaction conditions, making CFPS a powerful tool in biological research. It has been used for the expansion of genetic code, assembly of viruses, and in metabolic engineering for production of toxic and complex proteins. Subsequently, CFPS systems have emerged as potent technology for high-throughput production of membrane proteins, enzymes, and therapeutics. The present review highlights the recent advances and uses of CFPS systems in biomedical, therapeutic, and biotechnological applications. Additionally, we highlight possible solutions to the potential biosafety issues that may be encountered while using CFPS technology.
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Affiliation(s)
- Khushal Khambhati
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Gargi Bhattacharjee
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Nisarg Gohil
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | | | - Vishwesh Kulkarni
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Vijai Singh
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
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19
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Pellowe GA, Booth PJ. Structural insight into co-translational membrane protein folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183019. [PMID: 31302079 DOI: 10.1016/j.bbamem.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 11/30/2022]
Abstract
Membrane protein folding studies lag behind those of water-soluble proteins due to immense difficulties of experimental study, resulting from the need to provide a hydrophobic lipid-bilayer environment when investigated in vitro. A sound understanding of folding mechanisms is important for membrane proteins as they contribute to a third of the proteome and are frequently associated with disease when mutated and/or misfolded. Membrane proteins largely consist of α-helical, hydrophobic transmembrane domains, which insert into the membrane, often using the SecYEG/Sec61 translocase system. This mini-review highlights recent advances in techniques that can further our understanding of co-translational folding and notably, the structure and insertion of nascent chains as they emerge from translating ribosomes. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Grant A Pellowe
- Department of Chemistry, King's College London, 7 Trinity Street, SE1 1DB, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, 7 Trinity Street, SE1 1DB, London, UK.
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20
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Expanding biological applications using cell-free metabolic engineering: An overview. Metab Eng 2018; 50:156-172. [PMID: 30367967 DOI: 10.1016/j.ymben.2018.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/21/2022]
Abstract
Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.
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21
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Lipids modulate the insertion and folding of the nascent chains of alpha helical membrane proteins. Biochem Soc Trans 2018; 46:1355-1366. [PMID: 30190329 DOI: 10.1042/bst20170424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
Membrane proteins must be inserted into a membrane and folded into their correct structure to function correctly. This insertion occurs during translation and synthesis by the ribosome for most α-helical membrane proteins. Precisely how this co-translational insertion and folding occurs, and the role played by the surrounding lipids, is still not understood. Most of the work on the influence of the lipid environment on folding and insertion has focussed on denatured, fully translated proteins, and thus does not replicate folding during unidirectional elongation of nascent chains that occurs in the cell. This review aims to highlight recent advances in elucidating lipid composition and bilayer properties optimal for insertion and folding of nascent chains in the membrane and in the assembly of oligomeric proteins.
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22
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Uyeda A, Watanabe T, Hohsaka T, Matsuura T. Different protein localizations on the inner and outer leaflet of cell-sized liposomes using cell-free protein synthesis. Synth Biol (Oxf) 2018; 3:ysy007. [PMID: 32995515 PMCID: PMC7445883 DOI: 10.1093/synbio/ysy007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/02/2022] Open
Abstract
Membranes of living cells possess asymmetry. The inner and outer leaflets of the membrane consist of different phospholipid compositions, which are known to affect the function of membrane proteins, and the loss of the asymmetry has been reported to lead to cell apoptosis. In addition, different proteins are found on the inner and outer leaflets of the membrane, and they are essential for various biochemical reactions, including those related to signal transduction and cell morphology. While in vitro lipid bilayer reconstitution with asymmetric phospholipid compositions has been reported, the reconstitution of lipid bilayer where different proteins are localized in the inner and outer leaflet, thereby enables asymmetric protein localizations, has remained difficult. Herein, we developed a simple method to achieve this asymmetry using an in vitro transcription–translation system (IVTT). The method used a benzylguanine (BG) derivative-modified phospholipid, which forms a covalent bond with a snap-tag sequence. We show that purified snap-tagged protein can be localized to the cell-sized liposome surface via an interaction between BG and the snap-tag. We then show that IVTT-synthesized proteins can be located at the lipid membrane and that different proteins can be asymmetrically localized on the outer and inner leaflets of liposomes.
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Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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Rebuffet E, Frick A, Järvå M, Törnroth-Horsefield S. Cell-free production and characterisation of human uncoupling protein 1-3. Biochem Biophys Rep 2017; 10:276-281. [PMID: 28955755 PMCID: PMC5614671 DOI: 10.1016/j.bbrep.2017.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/04/2017] [Accepted: 04/07/2017] [Indexed: 11/22/2022] Open
Abstract
The uncoupling proteins (UCPs) leak protons across the inner mitochondrial membrane, thus uncoupling the proton gradient from ATP synthesis. The main known physiological role for this is heat generation by UCP1 in brown adipose tissue. However, UCPs are also believed to be important for protection against reactive oxygen species, fine-tuning of metabolism and have been suggested to be involved in disease states such as obesity, diabetes and cancer. Structural studies of UCPs have long been hampered by difficulties in sample preparation with neither expression in yeast nor refolding from inclusion bodies in E. coli yielding sufficient amounts of pure and stable protein. In this study, we have developed a protocol for cell-free expression of human UCP1, 2 and 3, resulting in 1 mg pure protein per 20 mL of expression media. Lauric acid, a natural UCP ligand, significantly improved protein thermal stability and was therefore added during purification. Secondary structure characterisation using circular dichroism spectroscopy revealed the proteins to consist of mostly α-helices, as expected. All three UCPs were able to bind GDP, a well-known physiological inhibitor, as shown by the Fluorescence Resonance Energy Transfer (FRET) technique, suggesting that the proteins are in a natively folded state. A protocol for cell-free expression of human uncoupling protein 1–3 is described. Addition of native membrane components increased expression levels. Addition of lauric acid increased protein stability in solution. CD spectroscopy confirms alpha-helical secondary structure as expected. All proteins binds GDP as demonstrated by Fluorescence Resonance Energy Transfer.
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Affiliation(s)
- Etienne Rebuffet
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Anna Frick
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Michael Järvå
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Susanna Törnroth-Horsefield
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden.,Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, 221 00 Lund, Sweden
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24
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Harris NJ, Reading E, Ataka K, Grzegorzewski L, Charalambous K, Liu X, Schlesinger R, Heberle J, Booth PJ. Structure formation during translocon-unassisted co-translational membrane protein folding. Sci Rep 2017; 7:8021. [PMID: 28808343 PMCID: PMC5556060 DOI: 10.1038/s41598-017-08522-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Correctly folded membrane proteins underlie a plethora of cellular processes, but little is known about how they fold. Knowledge of folding mechanisms centres on reversible folding of chemically denatured membrane proteins. However, this cannot replicate the unidirectional elongation of the protein chain during co-translational folding in the cell, where insertion is assisted by translocase apparatus. We show that a lipid membrane (devoid of translocase components) is sufficient for successful co-translational folding of two bacterial α-helical membrane proteins, DsbB and GlpG. Folding is spontaneous, thermodynamically driven, and the yield depends on lipid composition. Time-resolving structure formation during co-translational folding revealed different secondary and tertiary structure folding pathways for GlpG and DsbB that correlated with membrane interfacial and biological transmembrane amino acid hydrophobicity scales. Attempts to refold DsbB and GlpG from chemically denatured states into lipid membranes resulted in extensive aggregation. Co-translational insertion and folding is thus spontaneous and minimises aggregation whilst maximising correct folding.
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Affiliation(s)
- Nicola J Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Lucjan Grzegorzewski
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Kalypso Charalambous
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Xia Liu
- School of Biochemistry, Medical Sciences, University Walk, University of Bristol, Bristol, UK
| | - Ramona Schlesinger
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Paula J Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK.
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25
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Wei P, Wang Q, Hang B, Shi F, Cai J, Huang L, Xu Z. High-level cell-free expression and functional characterization of a novel aquaporin from Photobactetrium profundum SS9. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Salehi ASM, Smith MT, Schinn S, Hunt JM, Muhlestein C, Diray‐Arce J, Nielsen BL, Bundy BC. Efficient t
RNA
degradation and quantification in
Escherichia coli
cell extract using R
N
ase‐coated magnetic beads: A key step toward codon emancipation. Biotechnol Prog 2017; 33:1401-1407. [DOI: 10.1002/btpr.2511] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/03/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Amin S. M. Salehi
- Department of Chemical EngineeringBrigham Young UniversityProvo UT84602
| | - Mark T. Smith
- Department of Chemical EngineeringBrigham Young UniversityProvo UT84602
| | - Song‐Min Schinn
- Department of Chemical EngineeringBrigham Young UniversityProvo UT84602
| | - Jeremy M. Hunt
- Department of Chemical EngineeringBrigham Young UniversityProvo UT84602
| | | | - Joann Diray‐Arce
- Department of Microbiology & Molecular BiologyBrigham Young UniversityProvo UT84602
| | - Brent L. Nielsen
- Department of Microbiology & Molecular BiologyBrigham Young UniversityProvo UT84602
| | - Bradley C. Bundy
- Department of Chemical EngineeringBrigham Young UniversityProvo UT84602
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27
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Shilling PJ, Bumbak F, Scott DJ, Bathgate RAD, Gooley PR. Characterisation of a cell-free synthesised G-protein coupled receptor. Sci Rep 2017; 7:1094. [PMID: 28439124 PMCID: PMC5430785 DOI: 10.1038/s41598-017-01227-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/27/2017] [Indexed: 02/03/2023] Open
Abstract
G-protein coupled receptors are the largest family of integral membrane proteins found within the human genome. They function as receptors and modulators to a wide range of ligands and responses which are crucial for human health. GPCR study, specifically the investigation of structure and interaction to cognate ligands, is of high priority. Limitations for structural study can be traced in part, to obtaining suitable quantities of recombinant protein. We sought to address the limitations of traditional recombinant technologies by utilising an Escherichia coli based cell-free protein synthesis (CFPS) approach for production of a thermostable neurotensin receptor 1 (en2NTS1). Initial results were promising, with a high amount (up to 2 mg/mL) of en2NTS1 produced, that had attained correct secondary structure. Meanwhile, concurrent experiments indicated that CFPS produced en2NTS1 showed non-competitive binding to the peptide ligand neurotensin8-13 when compared to E. coli produced en2NTS1. 1H-13C HMQC SOFAST NMR spectra were indicative of disrupted tertiary structure for CFPS produced 13CH3-methionine labelled en2NTS1. The results obtained, indicate CFPS produced en2NTS1 is not forming a discrete tertiary structure and that further development of the CFPS technique needs to be carried out.
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Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
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28
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Salehi ASM, Shakalli Tang MJ, Smith MT, Hunt JM, Law RA, Wood DW, Bundy BC. Cell-Free Protein Synthesis Approach to Biosensing hTRβ-Specific Endocrine Disruptors. Anal Chem 2017; 89:3395-3401. [DOI: 10.1021/acs.analchem.6b04034] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amin S. M. Salehi
- Department
of Chemical Engineering, Brigham Young University, Provo, Utah 84602, United States
| | - Miriam J. Shakalli Tang
- Department
of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Mark T. Smith
- Department
of Chemical Engineering, Brigham Young University, Provo, Utah 84602, United States
| | - Jeremy M. Hunt
- Department
of Chemical Engineering, Brigham Young University, Provo, Utah 84602, United States
| | - Robert A. Law
- Department
of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - David W. Wood
- Department
of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Bradley C. Bundy
- Department
of Chemical Engineering, Brigham Young University, Provo, Utah 84602, United States
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29
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Lu Y. Cell-free synthetic biology: Engineering in an open world. Synth Syst Biotechnol 2017; 2:23-27. [PMID: 29062958 PMCID: PMC5625795 DOI: 10.1016/j.synbio.2017.02.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/06/2017] [Indexed: 10/26/2022] Open
Abstract
Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.
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Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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30
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Hunt JP, Yang SO, Wilding KM, Bundy BC. The growing impact of lyophilized cell-free protein expression systems. Bioengineered 2016; 8:325-330. [PMID: 27791452 DOI: 10.1080/21655979.2016.1241925] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recently reported shelf-stable, on-demand protein synthesis platforms are enabling new possibilities in biotherapeutics, biosensing, biocatalysis, and high throughput protein expression. Lyophilized cell-free protein expression systems not only overcome cold-storage limitations, but also enable stockpiling for on-demand synthesis and completely sterilize the protein synthesis platform. Recently reported high-yield synthesis of cytotoxic protein Onconase from lyophilized E. coli extract preparations demonstrates the utility of lyophilized cell-free protein expression and its potential for creating on-demand biotherapeutics, vaccines, biosensors, biocatalysts, and high throughput protein synthesis.
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Affiliation(s)
- J Porter Hunt
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Seung Ook Yang
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Kristen M Wilding
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
| | - Bradley C Bundy
- a Department of Chemical Engineering , Brigham Young University , Provo , Utah , USA
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31
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Georgi V, Georgi L, Blechert M, Bergmeister M, Zwanzig M, Wüstenhagen DA, Bier FF, Jung E, Kubick S. On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode. LAB ON A CHIP 2016; 16:269-81. [PMID: 26554896 DOI: 10.1039/c5lc00700c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Many pharmaceuticals are proteins or their development is based on proteins. Cell-free protein synthesis (CFPS) is an innovative alternative to conventional cell based systems which enables the production of proteins with complex and even new characteristics. However, the short lifetime, low protein production and expensive reagent costs are still limitations of CFPS. Novel automated microfluidic systems might allow continuous, controllable and resource conserving CFPS. The presented microfluidic TRITT platform (TRITT for Transcription - RNA Immobilization & Transfer - Translation) addresses the individual biochemical requirements of the transcription and the translation step of CFPS in separate compartments, and combines the reaction steps by quasi-continuous transfer of RNA templates to enable automated CFPS. In detail, specific RNA templates with 5' and 3' hairpin structures for stabilization against nucleases were immobilized during in vitro transcription by newly designed and optimized hybridization oligonucleotides coupled to magnetizable particles. Transcription compatibility and reusability for immobilization of these functionalized particles was successfully proven. mRNA transfer was realized on-chip by magnetic actuated particle transfer, RNA elution and fluid flow to the in vitro translation compartment. The applicability of the microfluidic TRITT platform for the production of the cytotoxic protein Pierisin with simultaneous incorporation of a non-canonical amino acid for fluorescence labeling was demonstrated. The new reaction mode (TRITT mode) is a modified linked mode that fulfills the precondition for an automated modular reactor system. By continual transfer of new mRNA, the novel procedure overcomes problems caused by nuclease digestion and hydrolysis of mRNA during TL in standard CFPS reactions.
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Affiliation(s)
- V Georgi
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany. and Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - L Georgi
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - M Blechert
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Bergmeister
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Zwanzig
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - D A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - F F Bier
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - E Jung
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - S Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
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32
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Salehi ASM, Smith MT, Bennett AM, Williams JB, Pitt WG, Bundy BC. Cell‐free protein synthesis of a cytotoxic cancer therapeutic: Onconase production and a just‐add‐water cell‐free system. Biotechnol J 2015; 11:274-81. [DOI: 10.1002/biot.201500237] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/30/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Amin S. M. Salehi
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Mark Thomas Smith
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Anthony M. Bennett
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Jacob B. Williams
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - William G. Pitt
- Department of Chemical Engineering Brigham Young University Provo Utah USA
| | - Bradley C. Bundy
- Department of Chemical Engineering Brigham Young University Provo Utah USA
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33
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Xu Y, Lee J, Tran C, Heibeck TH, Wang WD, Yang J, Stafford RL, Steiner AR, Sato AK, Hallam TJ, Yin G. Production of bispecific antibodies in "knobs-into-holes" using a cell-free expression system. MAbs 2015; 7:231-42. [PMID: 25427258 PMCID: PMC4623329 DOI: 10.4161/19420862.2015.989013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bispecific antibodies have emerged in recent years as a promising field of research for therapies in oncology, inflammable diseases, and infectious diseases. Their capability of dual target recognition allows for novel therapeutic hypothesis to be tested, where traditional mono-specific antibodies would lack the needed mode of target engagement. Among extremely diverse architectures of bispecific antibodies, knobs-into-holes (KIHs) technology, which involves engineering CH3 domains to create either a “knob” or a “hole” in each heavy chain to promote heterodimerization, has been widely applied. Here, we describe the use of a cell-free expression system (Xpress CF) to produce KIH bispecific antibodies in multiple scaffolds, including 2-armed heterodimeric scFv-KIH and one-armed asymmetric BiTE-KIH with tandem scFv. Efficient KIH production can be achieved by manipulating the plasmid ratio between knob and hole, and further improved by addition of prefabricated knob or hole. These studies demonstrate the versatility of Xpress CF in KIH production and provide valuable insights into KIH construct design for better assembly and expression titer.
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Key Words
- BiTE, bispecific T-cell engager
- BiTE-KIH
- CHO, Chinese hamster ovary
- ELISA, enzyme-linked immunosorbent assay
- EpCAM, epithelial cell adhesion molecule
- FACS, fluorescence-activated cell sorting
- Fab, antigen-binding fragment
- Fc, fragment crystallizable
- FcR, Fc receptor
- HC, immunoglobulin heavy chain
- HER2, human epidermal growth factor receptor 2
- IgG, immunoglobulin G
- KIH, knob-into-hole
- LC, immunoglobulin light chain
- LC-MS, liquid chromatography-mass spectrometry
- PK, pharmacokinetics
- bispecific antibody
- cell-free protein expression
- knob-into-hole
- prefabrication
- scFv, single-chain fragment variable
- scFv-KIH
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Affiliation(s)
- Yiren Xu
- a Sutro Biopharma, Inc. ; South San Francisco , CA USA
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34
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Abstract
The large-scale production of recombinant G protein-coupled receptors (GPCRs) is one of the major bottlenecks that hamper functional and structural studies of this important class of integral membrane proteins. Heterologous overexpression of GPCRs often results in low yields of active protein, usually due to a combination of several factors, such as low expression levels, protein insolubility, host cell toxicity, and the need to use harsh and often denaturing detergents (e.g., SDS, LDAO, OG, and DDM, among others) to extract the recombinant receptor from the host cell membrane. Many of these problematic issues are inherently linked to cell-based expression systems and can therefore be circumvented by the use of cell-free systems. In this unit, we provide a range of protocols for the production of GPCRs in a cell-free expression system. Using this system, we typically obtain GPCR expression levels of ∼1 mg per ml of reaction mixture in the continuous-exchange configuration. Although the protocols in this unit have been optimized for the cell-free expression of GPCRs, they should provide a good starting point for the production of other classes of membrane proteins, such as ion channels, aquaporins, carrier proteins, membrane-bound enzymes, and even large molecular complexes.
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Affiliation(s)
- Kenneth Segers
- VIB Center for the Biology of Disease, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.,Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
| | - Stefan Masure
- Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
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35
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Henrich E, Hein C, Dötsch V, Bernhard F. Membrane protein production in Escherichia coli cell-free lysates. FEBS Lett 2015; 589:1713-22. [PMID: 25937121 DOI: 10.1016/j.febslet.2015.04.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/01/2023]
Abstract
Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
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36
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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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37
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Henrich E, Dötsch V, Bernhard F. Screening for Lipid Requirements of Membrane Proteins by Combining Cell-Free Expression with Nanodiscs. Methods Enzymol 2015; 556:351-69. [DOI: 10.1016/bs.mie.2014.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Hein C, Henrich E, Orbán E, Dötsch V, Bernhard F. Hydrophobic supplements in cell-free systems: Designing artificial environments for membrane proteins. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300050] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Christopher Hein
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Erik Henrich
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Erika Orbán
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
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39
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A Comparative Study of α-Hemolysin Expression in Supported Lipid Bilayers of Synthetic and Enriched Complex Bacterial Lipid. BIONANOSCIENCE 2014. [DOI: 10.1007/s12668-014-0127-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Indiveri C, Galluccio M, Scalise M, Pochini L. Strategies of bacterial over expression of membrane transporters relevant in human health: the successful case of the three members of OCTN subfamily. Mol Biotechnol 2013; 54:724-36. [PMID: 22843325 PMCID: PMC3636443 DOI: 10.1007/s12033-012-9586-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The OCTN subfamily includes OCTN1, 2, and 3 which are structurally and functionally related. These transporters are involved in maintenance of the carnitine homeostasis, which is essential in mammals for fatty acid β-oxidation, VLDL assembly, post-translational modifications, and other essential functions. Indeed, defects of these transporters lead to severe pathologies. OCTN1 and OCTN2 are expressed in many human tissues, while OCTN3 gene has been identified only in mouse and rat. The transporters mediate transport of carnitine and other substrates with different efficiencies and mechanisms. In order to over express the three proteins, a screening of many combinations of E. coli strains with plasmid constructs has been conducted. Only Rosetta(DE3) or Rosettagami2(DE3) gave significant expression. Higher protein amounts were firstly obtained with pET-41a(+) or pGEX-4T1 carrying fusion protein tags which required additional purification passages. Vectors carrying only a 6His tag, suitable for single passage purification, were preferred even though they lead to lower initial expression levels. Expressions were then increased optimizing several critical parameters. hOCTN1 was obtained with pH6EX3 in RosettaGami2(DE3)pLysS. hOCTN2 and mOCTN3 were obtained using pET-21a(+) in Rosetta(DE3). In particular, hOCTN2 was expressed only after codon bias, substituting the second triplet CGG with AAA (R2K mutant). The best growth conditions for hOCTN1 and mOCTN3 were 28 °C and 6 h of induction, while 4 h of induction for hOCTN2R2K. The proteins collected in the insoluble fraction of cell lysates, solubilized with sarkosyl, were purified by Ni-chelating chromatography. Final yield was 2.0, 3.0, or 3.5 mg/l of cell culture for mOCTN3, hOCTN1, or hOCTN2R2K. The data indicated that, in spite of the close evolutionary relations, several factors play different critical roles in bacterial expression of the three proteins, thus general criteria cannot be underlined. However, the strategy of dealing with related proteins revealed to be finally successful for over expressing all the three subfamily members.
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Affiliation(s)
- Cesare Indiveri
- Department of Cell Biology, University of Calabria, Arcavacata di Rende, Italy.
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41
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Abstract
In vitro methods have enabled the rapid and efficient evolution of proteins and successful generation of novel and highly functional proteins. However, the available methods consider only globular proteins (e.g., antibodies, enzymes) and not membrane proteins despite the biological and pharmaceutical importance of the latter. In this study, we report the development of a method called liposome display that can evolve the properties of membrane proteins entirely in vitro. This method, which involves in vitro protein synthesis inside liposomes, which are cell-sized phospholipid vesicles, was applied to the pore-forming activity of α-hemolysin, a membrane protein derived from Staphylococcus aureus. The obtained α-hemolysin mutant possessed only two point mutations but exhibited a 30-fold increase in its pore-forming activity compared with the WT. Given the ability to synthesize various membrane proteins and modify protein synthesis and functional screening conditions, this method will allow for the rapid and efficient evolution of a wide range of membrane proteins.
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42
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Ritz S, Hulko M, Zerfass C, May S, Hospach I, Krasteva N, Nelles G, Sinner EK. Cell-free expression of a mammalian olfactory receptor and unidirectional insertion into small unilamellar vesicles (SUVs). Biochimie 2013; 95:1909-16. [PMID: 23816872 DOI: 10.1016/j.biochi.2013.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/20/2013] [Indexed: 01/29/2023]
Abstract
Although the identification of the multigene family encoding mammalian olfactory receptors were identified more than 20 years ago, we are far from understanding olfactory perception because of the difficulties in functional expression of these receptors in heterologous cell systems. Cell-free (CF) or in vitro expression systems offer an elegant alternative route to cell based protein expression, as the functional expression of membrane proteins can be directly achieved from the genetic template without the need of cell cultivation and protein isolation. Here we investigated in detail the cell-free expression and membrane insertion of the olfactory receptor OR5 in dependence of different experimental conditions like probing different origins of the cell-free expression system (from bacteria, via plants and insects toward mammalian system) and lipid composition of the respective extracts. We provided substantial biochemical indications by radioactive labeling based on [(35)S]-methionine, followed by proteolytic digestion, and we found that the insertion of the olfactory receptor OR5 into liposomes resulted in an unidirectional orientation with the binding side exposed into the aqueous space, resembling the native orientation in the cilia of the olfactory neurons. We report the different results in synthesis capacity for the different in vitro systems employed as we like to demonstrate the first in vitro kit toward and ex situ and ex vivo odorant receptor array.
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Affiliation(s)
- Sandra Ritz
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.
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43
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Lu Y, Welsh JP, Chan W, Swartz JR. Escherichia coli-based cell free production of flagellin and ordered flagellin display on virus-like particles. Biotechnol Bioeng 2013; 110:2073-85. [PMID: 23519642 DOI: 10.1002/bit.24903] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/24/2013] [Accepted: 03/04/2013] [Indexed: 11/06/2022]
Abstract
Bacterial flagellin has been explored as a potential vaccine adjuvant for enhancing immune responses. In this article, we describe Escherichia coli-based cell-free protein synthesis (CFPS) as a method to rapidly produce soluble phase 1 flagellin (FliC) protein from Salmonella typhimurium. The yield was about 300 µg/mL and the product had much higher affinity for the TLR5 receptor (EC50 = 2.4 ± 1.4 pM) than previously reported. The flagellin coding sequence was first optimized for cell-free expression. We then found that the D0 domain at the C-terminus of flagellin was susceptible to proteolytic degradation in the CFPS system. Proteolysis was reduced by protease inhibitors, the use of protease-deficient cell extracts or deletion of the flagellin D0 domain. A human Toll-Like Receptor 5 (hTLR5)-specific bioactivity analysis of purified flagellin demonstrated that, although the D0 domain is far from the TLR5 recognition region, it is important for flagellin bioactivity. We next incorporated a non-natural amino acid displaying an alkyne moiety into flagellin using the CFPS system and attached flagellin to hepatitis B core virus-like particles (VLPs) using bioorthogonal azide-alkyne cycloaddition reactions. The ordered and oriented VLP display of flagellin increased its specific TLR5 stimulation activity by approximately 10-fold.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, California 94305-5025, USA
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44
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Albayrak C, Swartz JR. Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation. Nucleic Acids Res 2013; 41:5949-63. [PMID: 23589624 PMCID: PMC3675464 DOI: 10.1093/nar/gkt226] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We describe a new cell-free protein synthesis (CFPS) method for site-specific incorporation of non-natural amino acids (nnAAs) into proteins in which the orthogonal tRNA (o-tRNA) and the modified protein (i.e. the protein containing the nnAA) are produced simultaneously. Using this method, 0.9–1.7 mg/ml of modified soluble super-folder green fluorescent protein (sfGFP) containing either p-azido-l-phenylalanine (pAzF) or p-propargyloxy-l-phenylalanine (pPaF) accumulated in the CFPS solutions; these yields correspond to 50–88% suppression efficiency. The o-tRNA can be transcribed either from a linearized plasmid or from a crude PCR product. Comparison of two different o-tRNAs suggests that the new platform is not limited by Ef-Tu recognition of the acylated o-tRNA at sufficiently high o-tRNA template concentrations. Analysis of nnAA incorporation across 12 different sites in sfGFP suggests that modified protein yields and suppression efficiencies (i.e. the position effect) do not correlate with any of the reported trends. Sites that were ineffectively suppressed with the original o-tRNA were better suppressed with an optimized o-tRNA (o-tRNAopt) that was evolved to be better recognized by Ef-Tu. This new platform can also be used to screen scissile ribozymes for improved catalysis.
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Affiliation(s)
- Cem Albayrak
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, CA 94305, USA
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45
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Albayrak C, Swartz JR. Using E. coli-based cell-free protein synthesis to evaluate the kinetic performance of an orthogonal tRNA and aminoacyl-tRNA synthetase pair. Biochem Biophys Res Commun 2013; 431:291-5. [DOI: 10.1016/j.bbrc.2012.12.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 12/13/2012] [Indexed: 11/30/2022]
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46
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Shadiac N, Nagarajan Y, Waters S, Hrmova M. Close allies in membrane protein research: Cell-free synthesis and nanotechnology. Mol Membr Biol 2013; 30:229-45. [DOI: 10.3109/09687688.2012.762125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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47
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Jaehme M, Michel H. Evaluation of cell-free protein synthesis for the crystallization of membrane proteins--a case study on a member of the glutamate transporter family from Staphylothermus marinus. FEBS J 2013; 280:1112-25. [PMID: 23279902 DOI: 10.1111/febs.12105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 12/07/2012] [Accepted: 12/18/2012] [Indexed: 12/25/2022]
Abstract
Cell-free in vitro synthesis of proteins using coupled transcription/translation is considered to be a powerful alternative to the use of traditional cell-based expression systems. Recently, promising developments have been reported applying cell-free production to membrane proteins for structural biology and in particular for NMR spectroscopy. However, the general applicability of this system to produce large amounts of stable, functional and homogeneous membrane proteins as required for X-ray crystallography remains to be determined. Here, we present a systematic study comparing structural and functional properties of membrane proteins produced using Escherichia coli derived in vitro and in vivo expression systems. The function of the target membrane protein, a previously uncharacterized bacterial glutamate transporter homolog from Staphylothermus marinus, was analyzed using ligand binding and transport assays. In addition, the protein structure was investigated with respect to its overall fold and oligomeric state in different detergents. We found that the protein synthesized in vitro is highly stable and monodisperse. However, in contrast to the protein produced using an in vivo system, it was not able to assemble into the native trimeric state nor to bind substrate. We thus conclude that cell-free expression systems can compromise folding and function of such complex secondary active transporters. The expression product has to be carefully characterized prior to biophysical investigations like crystallography of membrane proteins.
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Affiliation(s)
- Michael Jaehme
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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Cell-Free Systems: Functional Modules for Synthetic and Chemical Biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:67-102. [DOI: 10.1007/10_2013_185] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Roos C, Zocher M, Müller D, Münch D, Schneider T, Sahl HG, Scholz F, Wachtveitl J, Ma Y, Proverbio D, Henrich E, Dötsch V, Bernhard F. Characterization of co-translationally formed nanodisc complexes with small multidrug transporters, proteorhodopsin and with the E. coli MraY translocase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3098-106. [DOI: 10.1016/j.bbamem.2012.08.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
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Roos C, Kai L, Proverbio D, Ghoshdastider U, Filipek S, Dötsch V, Bernhard F. Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers. Mol Membr Biol 2012; 30:75-89. [PMID: 22716775 DOI: 10.3109/09687688.2012.693212] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Routine strategies for the cell-free production of membrane proteins in the presence of detergent micelles and for their efficient co-translational solubilization have been developed. Alternatively, the expression in the presence of rationally designed lipid bilayers becomes interesting in particular for biochemical studies. The synthesized membrane proteins would be directed into a more native-like environment and cell-free expression of transporters, channels or other membrane proteins in the presence of supplied artificial membranes could allow their subsequent functional analysis without any exposure to detergents. In addition, lipid-dependent effects on activity and stability of membrane proteins could systematically be studied. However, in contrast to the generally efficient detergent solubilization, the successful stabilization of membrane proteins with artificial membranes appears to be more difficult. A number of strategies have therefore been explored in order to optimize the co-translational association of membrane proteins with different forms of supplied lipid bilayers including liposomes, bicelles, microsomes or nanodiscs. In this review, we have compiled the current state-of-the-art of this technology and we summarize parameters which have been indicated as important for the co-translational association of cell-free synthesized membrane proteins with supplied membranes.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
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