1
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Knauer JF, Schulz C, Zemella A, Wüstenhagen DA, Walter RM, Küpper JH, Kubick S. Synthesis of mono Cytochrome P450 in a modified CHO-CPR cell-free protein production platform. Sci Rep 2024; 14:1271. [PMID: 38218994 PMCID: PMC10787779 DOI: 10.1038/s41598-024-51781-6] [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: 05/05/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Cytochromes P450 (CYPs) are a group of monooxygenases that can be found in almost all kinds of organisms. For CYPs to receive electrons from co-substrate NADPH, the activity of NADPH-Cytochrome-P450-oxidoreductase (CPR) is required as well. In humans, CYPs are an integral part of liver-based phase-1 biotransformation, which is essential for the metabolization of multiple xenobiotics and drugs. Consequently, CYPs are important players during drug development and therefore these enzymes are implemented in diverse screening applications. For these applications it is usually advantageous to use mono CYP microsomes containing only the CYP of interest. The generation of mono-CYP containing mammalian cells and vesicles is difficult since endogenous CYPs are present in many cell types that contain the necessary co-factors. By obtaining translationally active lysates from a modified CHO-CPR cell line, it is now possible to generate mono CYPs in a cell-free protein synthesis process in a straightforward manner. As a proof of principle, the synthesis of active human CYPs from three different CYP450 gene families (CYP1A2, CYP2B6 and CYP3A4), which are of outstanding interest in industry and academia was demonstrated. Luciferase based activity assays confirm the activity of the produced CYPs and enable the individual adaptation of the synthesis process for efficient cell-free enzyme production. Furthermore, they allow for substrate and inhibitor screenings not only for wild-type CYPs but also for mutants and further CYP isoforms and variants. As an example, the turnover of selected CYP substrates by cell-free synthesized CYPs was demonstrated via an indirect luciferase assay-based screening setup.
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Affiliation(s)
- Jan Felix Knauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
| | - Christian Schulz
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jan-Heiner Küpper
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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3
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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4
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Manzer ZA, Selivanovitch E, Ostwalt AR, Daniel S. Membrane protein synthesis: no cells required. Trends Biochem Sci 2023; 48:642-654. [PMID: 37087310 DOI: 10.1016/j.tibs.2023.03.006] [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: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ekaterina Selivanovitch
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexis R Ostwalt
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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5
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Tosaka T, Kamiya K. Function Investigations and Applications of Membrane Proteins on Artificial Lipid Membranes. Int J Mol Sci 2023; 24:ijms24087231. [PMID: 37108393 PMCID: PMC10138308 DOI: 10.3390/ijms24087231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Membrane proteins play an important role in key cellular functions, such as signal transduction, apoptosis, and metabolism. Therefore, structural and functional studies of these proteins are essential in fields such as fundamental biology, medical science, pharmacology, biotechnology, and bioengineering. However, observing the precise elemental reactions and structures of membrane proteins is difficult, despite their functioning through interactions with various biomolecules in living cells. To investigate these properties, methodologies have been developed to study the functions of membrane proteins that have been purified from biological cells. In this paper, we introduce various methods for creating liposomes or lipid vesicles, from conventional to recent approaches, as well as techniques for reconstituting membrane proteins into artificial membranes. We also cover the different types of artificial membranes that can be used to observe the functions of reconstituted membrane proteins, including their structure, number of transmembrane domains, and functional type. Finally, we discuss the reconstitution of membrane proteins using a cell-free synthesis system and the reconstitution and function of multiple membrane proteins.
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Affiliation(s)
- Toshiyuki Tosaka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Gunma 376-8515, Japan
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6
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Haueis L, Stech M, Schneider E, Lanz T, Hebel N, Zemella A, Kubick S. Rapid One-Step Capturing of Native, Cell-Free Synthesized and Membrane-Embedded GLP-1R. Int J Mol Sci 2023; 24:ijms24032808. [PMID: 36769142 PMCID: PMC9917595 DOI: 10.3390/ijms24032808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are of outstanding pharmacological interest as they are abundant in cell membranes where they perform diverse functions that are closely related to the vitality of cells. The analysis of GPCRs in natural membranes is laborious, as established methods are almost exclusively cell culture-based and only a few methods for immobilization in a natural membrane outside the cell are known. Within this study, we present a one-step, fast and robust immobilization strategy of the GPCR glucagon-like peptide 1 receptor (GLP-1R). GLP-1R was synthesized in eukaryotic lysates harboring endogenous endoplasmic reticulum-derived microsomes enabling the embedment of GLP-1R in a natural membrane. Interestingly, we found that these microsomes spontaneously adsorbed to magnetic Neutravidin beads thus providing immobilized membrane protein preparations which required no additional manipulation of the target receptor or its supporting membrane. The accessibility of the extracellular domain of membrane-embedded and bead-immobilized GLP-1R was demonstrated by bead-based enzyme-linked immunosorbent assay (ELISA) using GLP-1R-specific monoclonal antibodies. In addition, ligand binding of immobilized GLP-1R was verified in a radioligand binding assay. In summary, we present an easy and straightforward synthesis and immobilization methodology of an active GPCR which can be beneficial for studying membrane proteins in general.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Correspondence:
| | | | - Thorsten Lanz
- 3B Pharmaceuticals GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Nicole Hebel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
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7
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Harris NJ, Pellowe GA, Blackholly LR, Gulaidi-Breen S, Findlay HE, Booth PJ. Methods to study folding of alpha-helical membrane proteins in lipids. Open Biol 2022; 12:220054. [PMID: 35855589 PMCID: PMC9297032 DOI: 10.1098/rsob.220054] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How alpha-helical membrane proteins fold correctly in the highly hydrophobic membrane interior is not well understood. Their folding is known to be highly influenced by the lipids within the surrounding bilayer, but the majority of folding studies have focused on detergent-solubilized protein rather than protein in a lipid environment. There are different ways to study folding in lipid bilayers, and each method has its own advantages and disadvantages. This review will discuss folding methods which can be used to study alpha-helical membrane proteins in bicelles, liposomes, nanodiscs or native membranes. These folding methods include in vitro folding methods in liposomes such as denaturant unfolding studies, and single-molecule force spectroscopy studies in bicelles, liposomes and native membranes. This review will also discuss recent advances in co-translational folding studies, which use cell-free expression with liposomes or nanodiscs or are performed in vivo with native membranes.
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Affiliation(s)
- Nicola J. Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A. Pellowe
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Laura R. Blackholly
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | | | - Heather E. Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paula J. Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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8
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Haueis L, Stech M, Kubick S. A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies. Front Bioeng Biotechnol 2022; 10:896763. [PMID: 35573250 PMCID: PMC9096027 DOI: 10.3389/fbioe.2022.896763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, ∼15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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9
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Harris NJ, Reading E, Booth PJ. Cell-Free Synthesis Strategies to Probe Co-translational Folding of Proteins Within Lipid Membranes. Methods Mol Biol 2022; 2433:273-292. [PMID: 34985751 DOI: 10.1007/978-1-0716-1998-8_17] [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] [Indexed: 06/14/2023]
Abstract
In order to comprehend the molecular basis of transmembrane protein biogenesis, methods are required that are capable of investigating the co-translational folding of these hydrophobic proteins. Equally, in artificial cell studies, controllable methods are desirable for in situ synthesis of membrane proteins that then direct reactions in the synthetic cell membrane. Here we describe a method that exploits cell-free expression systems and tunable membrane mimetics to facilitate co-translational studies. Alteration of the lipid bilayer composition improves the efficiency of the folding system. The approach also enables membrane transport proteins to be made and inserted into artificial cell platforms such as droplet interface bilayers. Importantly, this gives a new facet to the droplet networks by enabling specific transport of molecules across the synthetic bilayer against a concentration gradient. This method also includes a protocol to pause and restart translation of membrane proteins at specified positions during their co-translational folding. This stop-start strategy provides an avenue to investigate whether the proteins fold in sequence order, or if the correct fold of N-terminal regions is reliant on the synthesis of downstream residues.
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Affiliation(s)
| | - Eamonn Reading
- Department of Chemistry, King's College London, London, UK
| | - Paula J Booth
- Department of Chemistry, King's College London, London, UK.
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10
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Batista AC, Soudier P, Kushwaha M, Faulon J. Optimising protein synthesis in cell‐free systems, a review. ENGINEERING BIOLOGY 2021; 5:10-19. [PMID: 36968650 PMCID: PMC9996726 DOI: 10.1049/enb2.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.
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Affiliation(s)
- Angelo C. Batista
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Paul Soudier
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Manish Kushwaha
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Jean‐Loup Faulon
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
- SYNBIOCHEM Center School of Chemistry Manchester Institute of Biotechnology The University of Manchester Manchester UK
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11
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Boyd MA, Kamat NP. Designing Artificial Cells towards a New Generation of Biosensors. Trends Biotechnol 2020; 39:927-939. [PMID: 33388162 DOI: 10.1016/j.tibtech.2020.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 01/31/2023]
Abstract
The combination of biological and synthetic materials has great potential to generate new types of biosensors. Toward this goal, recent advances in artificial cell development have demonstrated the capacity to detect a variety of analytes and environmental changes by encapsulating genetically encoded sensors within bilayer membranes, expanding the contexts within which biologically based sensing can operate. This chassis not only acts as a container for cell-free sensors, but can also play an active role in artificial cell sensing by serving as an additional gate mediating the transfer of environmental information. Here, we focus on recent progress toward stimuli-responsive artificial cells and discuss strategies for membrane functionalization in order to expand cell-free biosensing capabilities and applications.
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Affiliation(s)
- Margrethe A Boyd
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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12
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Abarghooi Kahaki F, Monzavi S, Bamehr H, Bandani E, Payandeh Z, Jahangiri A, Khalili S. Expression and Purification of Membrane Proteins in Different Hosts. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-10009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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14
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Abstract
Proteins are the main source of drug targets and some of them possess therapeutic potential themselves. Among them, membrane proteins constitute approximately 50% of the major drug targets. In the drug discovery pipeline, rapid methods for producing different classes of proteins in a simple manner with high quality are important for structural and functional analysis. Cell-free systems are emerging as an attractive alternative for the production of proteins due to their flexible nature without any cell membrane constraints. In a bioproduction context, open systems based on cell lysates derived from different sources, and with batch-to-batch consistency, have acted as a catalyst for cell-free synthesis of target proteins. Most importantly, proteins can be processed for downstream applications like purification and functional analysis without the necessity of transfection, selection, and expansion of clones. In the last 5 years, there has been an increased availability of new cell-free lysates derived from multiple organisms, and their use for the synthesis of a diverse range of proteins. Despite this progress, major challenges still exist in terms of scalability, cost effectiveness, protein folding, and functionality. In this review, we present an overview of different cell-free systems derived from diverse sources and their application in the production of a wide spectrum of proteins. Further, this article discusses some recent progress in cell-free systems derived from Chinese hamster ovary and Sf21 lysates containing endogenous translocationally active microsomes for the synthesis of membrane proteins. We particularly highlight the usage of internal ribosomal entry site sequences for more efficient protein production, and also the significance of site-specific incorporation of non-canonical amino acids for labeling applications and creation of antibody drug conjugates using cell-free systems. We also discuss strategies to overcome the major challenges involved in commercializing cell-free platforms from a laboratory level for future drug development.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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15
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Grimmer M, Bacia K. Giant Endoplasmic Reticulum vesicles (GERVs), a novel model membrane tool. Sci Rep 2020; 10:3100. [PMID: 32080222 PMCID: PMC7033103 DOI: 10.1038/s41598-020-59700-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Artificial giant vesicles have proven highly useful as membrane models in a large variety of biophysical and biochemical studies. They feature accessibility for manipulation and detection, but lack the compositional complexity needed to reconstitute complicated cellular processes. For the plasma membrane (PM), this gap was bridged by the establishment of giant PM vesicles (GPMVs). These native membranes have facilitated studies of protein and lipid diffusion, protein interactions, electrophysiology, fluorescence analysis of lateral domain formation and protein and lipid partitioning as well as mechanical membrane properties and remodeling. The endoplasmic reticulum (ER) is key to a plethora of biological processes in any eukaryotic cell. However, its intracellular location and dynamic and intricate tubular morphology makes it experimentally even less accessible than the PM. A model membrane, which will allow the afore-mentioned types of studies on GPMVs to be performed on ER membranes outside the cell, is therefore genuinely needed. Here, we introduce the formation of giant ER vesicles, termed GERVs, as a new tool for biochemistry and biophysics. To obtain GERVs, we have isolated ER membranes from Saccharomyces cerevisiae and fused them by exploiting the atlastin-like fusion protein Sey1p. We demonstrate the production of GERVs and their utility for further studies.
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Affiliation(s)
- Mona Grimmer
- Biophysical Chemistry, Institute of Chemistry, Charles-Tanford Protein Center, University of Halle, Kurt-Mothes-Str. 3 A, 06120, Halle, Germany
| | - Kirsten Bacia
- Biophysical Chemistry, Institute of Chemistry, Charles-Tanford Protein Center, University of Halle, Kurt-Mothes-Str. 3 A, 06120, Halle, Germany.
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16
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Screening and Identification of Novel cGAS Homologues Using a Combination of in Vitro and In Vivo Protein Synthesis. Int J Mol Sci 2019; 21:ijms21010105. [PMID: 31877895 PMCID: PMC6981698 DOI: 10.3390/ijms21010105] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 11/17/2022] Open
Abstract
The cyclic GMP-AMP synthase (cGAS) catalyzes the synthesis of the multifunctional second messenger, cGAMP, in metazoans. Although numerous cGAS homologues are predicted in protein databases, the catalytic activity towards cGAMP synthesis has been proven for only four of them. Therefore, we selected five novel and yet uncharacterized cGAS homologues, which cover a broad range in the field of vertebrates. Cell-free protein synthesis (CFPS) was used for a pre-screening to investigate if the cGAS genes originating from higher organisms can be efficiently expressed in a bacterial expression system. As all tested cGAS variants were expressible, enzymes were synthesized in vivo to supply higher amounts for a subsequent in vitro activity assay. The assays were carried out with purified enzymes and revealed vast differences in the activity of the homologues. For the first time, the cGAS homologues from the Przewalski's horse, naked mole-rat, bald eagle, and zebrafish were proven to catalyze the synthesis of cGAMP. The extension of the list of described cGAS variants enables the acquisition of further knowledge about the structural and molecular mechanism of cGAS, potentially leading to functional improvement of the enzyme.
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17
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Huber MC, Schreiber A, Schiller SM. Minimalist Protocell Design: A Molecular System Based Solely on Proteins that Form Dynamic Vesicular Membranes Embedding Enzymatic Functions. Chembiochem 2019; 20:2618-2632. [PMID: 31183952 DOI: 10.1002/cbic.201900283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Life in its molecular context is characterized by the challenge of orchestrating structure, energy and information processes through compartmentalization and chemical transformations amenable to mimicry of protocell models. Here we present an alternative protocell model incorporating dynamic membranes based on amphiphilic elastin-like proteins (ELPs) rather than phospholipids. For the first time we demonstrate the feasibility of combining vesicular membrane formation and biocatalytic activity with molecular entities of a single class: proteins. The presented self-assembled protein-membrane-based compartments (PMBCs) accommodate either an anabolic reaction, based on free DNA ligase as an example of information transformation processes, or a catabolic process. We present a catabolic process based on a single molecular entity combining an amphiphilic protein with tobacco etch virus (TEV) protease as part of the enclosure of a reaction space and facilitating selective catalytic transformations. Combining compartmentalization and biocatalytic activity by utilizing an amphiphilic molecular building block with and without enzyme functionalization enables new strategies in bottom-up synthetic biology, regenerative medicine, pharmaceutical science and biotechnology.
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Affiliation(s)
- Matthias C Huber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
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18
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Li J, Liu X, Man Y, Chen Q, Pei D, Wu W. Cell-free expression, purification and characterization of Drosophila melanogaster odorant receptor OR42a and its co-receptor. Protein Expr Purif 2019; 159:27-33. [PMID: 30872132 DOI: 10.1016/j.pep.2019.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 01/06/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Olfactory receptors (OR), a group of classic membrane proteins, plays a vital role in insect reproduction and acclimatization. Deciphering the molecular mechanism of insect olfaction could enhance pest control and environmental protection. Studies on ORs have faced a major bottleneck due to the notoriously strong hydrophobicity of ORs, which results in difficult expression in heterologous cell systems. Here, we demonstrated that insect ORs could be functionally produced using the E. coli cell-free protein synthesis system (CFPS), in which the highest yield of total ORs is 350 μg per 1 ml reaction. We tested the effects of detergent types and concentrations on soluble expression of ORs. The ORs showed a classic α-helical infrared spectrum. Quartz crystal microbalance (QCM) was used to demonstrate that ORs fold correctly and respond to their ligands. This is the first report that insect OR42a could be functionally produced in vitro. This approach may facilitate the development of biomimetic olfactory biosensors and may also be utilized for drug positioning and development, environmental protection and agriculture.
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Affiliation(s)
- Jianyong Li
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Xingping Liu
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Yahui Man
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Qian Chen
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Di Pei
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Wenjian Wu
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China.
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19
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Abstract
Cell-free protein synthesis (CFPS) has become an established tool for rapid protein synthesis in order to accelerate the discovery of new enzymes and the development of proteins with improved characteristics. Over the past years, progress in CFPS system preparation has been made towards simplification, and many applications have been developed with regard to tailor-made solutions for specific purposes. In this review, various preparation methods of CFPS systems are compared and the significance of individual supplements is assessed. The recent applications of CFPS are summarized and the potential for biocatalyst development discussed. One of the central features is the high-throughput synthesis of protein variants, which enables sophisticated approaches for rapid prototyping of enzymes. These applications demonstrate the contribution of CFPS to enhance enzyme functionalities and the complementation to in vivo protein synthesis. However, there are different issues to be addressed, such as the low predictability of CFPS performance and transferability to in vivo protein synthesis. Nevertheless, the usage of CFPS for high-throughput enzyme screening has been proven to be an efficient method to discover novel biocatalysts and improved enzyme variants.
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20
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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: 15] [Impact Index Per Article: 2.5] [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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21
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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22
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Damiati S, Kompella UB, Damiati SA, Kodzius R. Microfluidic Devices for Drug Delivery Systems and Drug Screening. Genes (Basel) 2018; 9:E103. [PMID: 29462948 PMCID: PMC5852599 DOI: 10.3390/genes9020103] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Uday B Kompella
- Department of Pharmaceutical Sciences, Ophthalmology, and Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Safa A Damiati
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Materials Genome Institute, Shanghai University, Shanghai 200444, China.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
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23
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Sonnabend A, Spahn V, Stech M, Zemella A, Stein C, Kubick S. Production of G protein-coupled receptors in an insect-based cell-free system. Biotechnol Bioeng 2017; 114:2328-2338. [PMID: 28574582 PMCID: PMC5599999 DOI: 10.1002/bit.26346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 04/21/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
The biochemical analysis of human cell membrane proteins remains a challenging task due to the difficulties in producing sufficient quantities of functional protein. G protein‐coupled receptors (GPCRs) represent a main class of membrane proteins and drug targets, which are responsible for a huge number of signaling processes regulating various physiological functions in living cells. To circumvent the current bottlenecks in GPCR studies, we propose the synthesis of GPCRs in eukaryotic cell‐free systems based on extracts generated from insect (Sf21) cells. Insect cell lysates harbor the fully active translational and translocational machinery allowing posttranslational modifications, such as glycosylation and phosphorylation of de novo synthesized proteins. Here, we demonstrate the production of several GPCRs in a eukaryotic cell‐free system, performed within a short time and in a cost‐effective manner. We were able to synthesize a variety of GPCRs ranging from 40 to 133 kDa in an insect‐based cell‐free system. Moreover, we have chosen the μ opioid receptor (MOR) as a model protein to analyze the ligand binding affinities of cell‐free synthesized MOR in comparison to MOR expressed in a human cell line by “one‐point” radioligand binding experiments. Biotechnol. Bioeng. 2017;114: 2328–2338. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Viola Spahn
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Christoph Stein
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
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24
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Zemella A, Grossmann S, Sachse R, Sonnabend A, Schaefer M, Kubick S. Qualifying a eukaryotic cell-free system for fluorescence based GPCR analyses. Sci Rep 2017. [PMID: 28623260 PMCID: PMC5473880 DOI: 10.1038/s41598-017-03955-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Membrane proteins are key elements in cell-mediated processes. In particular, G protein-coupled receptors (GPCRs) have attracted increasing interest since they affect cellular signaling. Furthermore, mutations in GPCRs can cause acquired and inheritable diseases. Up to date, there still exist a number of GPCRs that has not been structurally and functionally analyzed due to difficulties in cell-based membrane protein production. A promising approach for membrane protein synthesis and analysis has emerged during the last years and is known as cell-free protein synthesis (CFPS). Here, we describe a simply portable method to synthesize GPCRs and analyze their ligand-binding properties without the requirement of additional supplements such as liposomes or nanodiscs. This method is based on eukaryotic cell lysates containing translocationally active endogenous endoplasmic reticulum-derived microsomes where the insertion of GPCRs into biologically active membranes is supported. In this study we present CFPS in combination with fast fluorescence-based screening methods to determine the localization, orientation and ligand-binding properties of the endothelin B (ET-B) receptor upon expression in an insect-based cell-free system. To determine the functionality of the cell-free synthesized ET-B receptor, we analyzed the binding of its ligand endothelin-1 (ET-1) in a qualitative fluorescence-based assay and in a quantitative radioligand binding assay.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Solveig Grossmann
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Rita Sachse
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Michael Schaefer
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany.
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25
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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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26
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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27
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Thoring L, Wüstenhagen DA, Borowiak M, Stech M, Sonnabend A, Kubick S. Cell-Free Systems Based on CHO Cell Lysates: Optimization Strategies, Synthesis of "Difficult-to-Express" Proteins and Future Perspectives. PLoS One 2016; 11:e0163670. [PMID: 27684475 PMCID: PMC5042383 DOI: 10.1371/journal.pone.0163670] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/11/2016] [Indexed: 11/18/2022] Open
Abstract
Nowadays, biotechnological processes play a pivotal role in target protein production. In this context, Chinese Hamster Ovary (CHO) cells are one of the most prominent cell lines for the expression of recombinant proteins and revealed as a safe host for nearly 40 years. Nevertheless, the major bottleneck of common in vivo protein expression platforms becomes obvious when looking at the production of so called “difficult-to-express” proteins. This class of proteins comprises in particular several ion channels and multipass membrane proteins as well as cytotoxic proteins. To enhance the production of “difficult-to-express” proteins, alternative technologies were developed, mainly based on translationally active cell lysates. These so called “cell-free” protein synthesis systems enable an efficient production of different classes of proteins. Eukaryotic cell-free systems harboring endogenous microsomal structures for the synthesis of functional membrane proteins and posttranslationally modified proteins are of particular interest for future applications. Therefore, we present current developments in cell-free protein synthesis based on translationally active CHO cell extracts, underlining the high potential of this platform. We present novel results highlighting the optimization of protein yields, the synthesis of various “difficult-to-express” proteins and the cotranslational incorporation of non-standard amino acids, which was exemplarily demonstrated by residue specific labeling of the glycoprotein Erythropoietin and the multimeric membrane protein KCSA.
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Affiliation(s)
- Lena Thoring
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Doreen A. Wüstenhagen
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Maria Borowiak
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Marlitt Stech
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
| | - Andrei Sonnabend
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin
| | - Stefan Kubick
- Department of Cell-free and Cell-based Bioproduction, Branch Bioanalysis and Bioprocesses, Fraunhofer-Institute for Cell Therapy and Immunology (IZI-BB), Potsdam-Golm, Germany
- * E-mail:
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28
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Hartel AJW, Glogger M, Jones NG, Abuillan W, Batram C, Hermann A, Fenz SF, Tanaka M, Engstler M. N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold. Nat Commun 2016; 7:12870. [PMID: 27641538 PMCID: PMC5031801 DOI: 10.1038/ncomms12870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 01/17/2023] Open
Abstract
The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.
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Affiliation(s)
- Andreas J. W. Hartel
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Marius Glogger
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Nicola G. Jones
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
| | - Christopher Batram
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Anne Hermann
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Susanne F. Fenz
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, Heidelberg 69120, Germany
- Institute for Integrated Cell-Material Science (WPI iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Markus Engstler
- Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
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29
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Merk H, Rues RB, Gless C, Beyer K, Dong F, Dötsch V, Gerrits M, Bernhard F. Biosynthesis of membrane dependent proteins in insect cell lysates: identification of limiting parameters for folding and processing. Biol Chem 2016; 396:1097-107. [PMID: 25999328 DOI: 10.1515/hsz-2015-0105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022]
Abstract
G protein-coupled receptors, like many other membrane proteins, are notoriously difficult to synthesize in conventional cellular systems. Although expression in insect cells is considered the preferred technique for structural characterizations in particular, inefficient membrane translocation, instability, toxic effects and low yields still pose clear limitations for their production in living cells. Recent studies started to explore alternative strategies for the in vitro production of problematic membrane proteins in cell-free lysates in combination with supplied membranes. We provide a detailed study on the production efficiencies and quality of G protein-coupled receptors, Fab fragments and other proteins synthesized in insect cell lysates containing endogenous microsomes. Effects of different reaction kinetics, redox conditions and sample preparations on the specific activities of synthesized proteins have been analyzed. The extent of glycosylation, membrane translocation and percentages of ligand binding active fractions of synthesized protein samples have been determined. We provide strong evidence that membrane insertion of integral membrane proteins can represent a prime limiting factor for their preparative scale in vitro production. Improved expression protocols resulting into higher production rates yielded more active protein in case of Fab fragments, but not in case of the human endothelin B receptor.
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30
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Pathogen receptor discovery with a microfluidic human membrane protein array. Proc Natl Acad Sci U S A 2016; 113:4344-9. [PMID: 27044079 DOI: 10.1073/pnas.1518698113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The discovery of how a pathogen invades a cell requires one to determine which host cell receptors are exploited. This determination is a challenging problem because the receptor is invariably a membrane protein, which represents an Achilles heel in proteomics. We have developed a universal platform for high-throughput expression and interaction studies of membrane proteins by creating a microfluidic-based comprehensive human membrane protein array (MPA). The MPA is, to our knowledge, the first of its kind and offers a powerful alternative to conventional proteomics by enabling the simultaneous study of 2,100 membrane proteins. We characterized direct interactions of a whole nonenveloped virus (simian virus 40), as well as those of the hepatitis delta enveloped virus large form antigen, with candidate host receptors expressed on the MPA. Selected newly discovered membrane protein-pathogen interactions were validated by conventional methods, demonstrating that the MPA is an important tool for cellular receptor discovery and for understanding pathogen tropism.
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31
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Schmitt C, Lippert AH, Bonakdar N, Sandoghdar V, Voll LM. Compartmentalization and Transport in Synthetic Vesicles. Front Bioeng Biotechnol 2016; 4:19. [PMID: 26973834 PMCID: PMC4770187 DOI: 10.3389/fbioe.2016.00019] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/11/2016] [Indexed: 12/03/2022] Open
Abstract
Nanoscale vesicles have become a popular tool in life sciences. Besides liposomes that are generated from phospholipids of natural origin, polymersomes fabricated of synthetic block copolymers enjoy increasing popularity, as they represent more versatile membrane building blocks that can be selected based on their specific physicochemical properties, such as permeability, stability, or chemical reactivity. In this review, we focus on the application of simple and nested artificial vesicles in synthetic biology. First, we provide an introduction into the utilization of multicompartmented vesosomes as compartmentalized nanoscale bioreactors. In the bottom-up development of protocells from vesicular nanoreactors, the specific exchange of pathway intermediates across compartment boundaries represents a bottleneck for future studies. To date, most compartmented bioreactors rely on unspecific exchange of substrates and products. This is either based on changes in permeability of the coblock polymer shell by physicochemical triggers or by the incorporation of unspecific porin proteins into the vesicle membrane. Since the incorporation of membrane transport proteins into simple and nested artificial vesicles offers the potential for specific exchange of substances between subcompartments, it opens new vistas in the design of protocells. Therefore, we devote the main part of the review to summarize the technical advances in the use of phospholipids and block copolymers for the reconstitution of membrane proteins.
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Affiliation(s)
- Christine Schmitt
- Division of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna H. Lippert
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Navid Bonakdar
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Vahid Sandoghdar
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Lars M. Voll
- Division of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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32
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Moreno-Flores S. Inward multivesiculation at the basal membrane of adherent giant phospholipid vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:793-9. [PMID: 26828120 DOI: 10.1016/j.bbamem.2016.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 11/16/2022]
Abstract
Adherent giant vesicles composed of phosphatidylcholine, phosphatidylserine and biotinylated lipids form clusters of inward spherical buds at their basal membrane. The process is spontaneous and occurs when the vesicles undergo a sequence of osmotic swelling and deswelling. The daughter vesicles have a uniform size (diameter ≈ 2-3 μm), engulf small volumes of outer fluid and remain attached to the region of the membrane from which they generate, even after restoring the isotonicity. A pinning-sealing mechanism of long-wavelength modes of membrane fluctuations is proposed, by which the just-deflated vesicles reduce the surplus of membrane area and avoid excessive spreading and compression via biotin anchors. The work discusses the rationale behind the mechanism that furnishes GUVs with basal endovesicles, and its prospective use to simulate cellular events or to create molecular carriers.
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Affiliation(s)
- Susana Moreno-Flores
- Former affiliation: Institute for Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences (BOKU) Vienna, Muthgasse 11, A-1190, Vienna, Austria.
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33
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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: 31] [Impact Index Per Article: 3.9] [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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34
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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35
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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: 54] [Impact Index Per Article: 6.0] [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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Rues RB, Orbán E, Dötsch V, Bernhard F. Cell-free expression of G-protein coupled receptors: new pipelines for challenging targets. Biol Chem 2014; 395:1425-34. [DOI: 10.1515/hsz-2014-0217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/25/2014] [Indexed: 11/15/2022]
Abstract
Abstract
Based on their eminent importance for medical applications, G-protein coupled receptors are currently amongst the most frequently membrane protein targets analyzed by cell-free expression. The cell-free expression approach removes most bottlenecks known from conventional cell-based protein production pipelines and ensures fast access to a selected receptor target. In addition, receptors can be synthesized in presence of a large variety of artificial solubilization environments comprising detergents, lipids, nanodiscs and other amphiphilic compounds. The currently accumulated data based on a variety of analyzed receptors already opens promising perspectives for applications of cell-free synthesized samples in functional characterization and drug screening. Structural evaluation still suffers from high conformational dynamics causing sample instability and might be addressed in future by molecular engineering or immuno-stabilization approaches.
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37
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Developing cell-free protein synthesis systems: a focus on mammalian cells. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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38
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Stech M, Hust M, Schulze C, Dübel S, Kubick S. Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng Life Sci 2014; 14:387-398. [PMID: 25821419 PMCID: PMC4374706 DOI: 10.1002/elsc.201400036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 01/27/2023] Open
Abstract
Open cell-free translation systems based on Escherichia coli cell lysates have successfully been used to produce antibodies and antibody fragments. In this study, we demonstrate the cell-free expression of functional single-chain antibody variable fragments (scFvs) in a eukaryotic and endotoxin-free in vitro translation system based on Spodoptera frugiperda (Sf21) insect cell extracts. Three scFv candidates with different specificities were chosen as models. The first scFv candidate SH527-IIA4 specifically discriminates between its phosphorylated (SMAD2-P) and nonphosphorylated antigens (SMAD2) (where SMAD is mothers against decapentaplegic homolog 2), whereas the second scFv candidate SH527-IIC10 recognizes both, SMAD2-P and SMAD2. The third scFv candidate SH855-C11 binds specifically to a linear epitope of the CXC chemokine receptor type 5. The translocation of antibody fragments into the lumen of endogenous microsomal vesicles, which are contained in the lysate, was facilitated by fusion of scFv genes to the insect cell specific signal sequence of honeybee melittin. We compared the binding capabilities of scFv fragments with and without melittin signal peptide and detected that translocated scFv fragments were highly functional, whereas scFvs synthesized in the cytosol of the cell extract showed strongly decreased binding capabilities. Additionally, we describe a cell-free protein synthesis method for the incorporation of noncanonical amino acids into scFv molecules in eukaryotic cell lysates. We demonstrate the successful cotranslational labeling of de novo synthesized scFv molecules with fluorescent amino acids, using residue-specific as well as site-specific labeling.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Corina Schulze
- Department of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, University of Applied Sciences Berlin, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Braunschweig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm Potsdam, Germany
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39
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Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S. Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes. FEBS Lett 2014; 588:2774-81. [DOI: 10.1016/j.febslet.2014.06.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
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40
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Stech M, Quast RB, Sachse R, Schulze C, Wüstenhagen DA, Kubick S. A continuous-exchange cell-free protein synthesis system based on extracts from cultured insect cells. PLoS One 2014; 9:e96635. [PMID: 24804975 PMCID: PMC4013096 DOI: 10.1371/journal.pone.0096635] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/09/2014] [Indexed: 11/22/2022] Open
Abstract
In this study, we present a novel technique for the synthesis of complex prokaryotic and eukaryotic proteins by using a continuous-exchange cell-free (CECF) protein synthesis system based on extracts from cultured insect cells. Our approach consists of two basic elements: First, protein synthesis is performed in insect cell lysates which harbor endogenous microsomal vesicles, enabling a translocation of de novo synthesized target proteins into the lumen of the insect vesicles or, in the case of membrane proteins, their embedding into a natural membrane scaffold. Second, cell-free reactions are performed in a two chamber dialysis device for 48 h. The combination of the eukaryotic cell-free translation system based on insect cell extracts and the CECF translation system results in significantly prolonged reaction life times and increased protein yields compared to conventional batch reactions. In this context, we demonstrate the synthesis of various representative model proteins, among them cytosolic proteins, pharmacological relevant membrane proteins and glycosylated proteins in an endotoxin-free environment. Furthermore, the cell-free system used in this study is well-suited for the synthesis of biologically active tissue-type-plasminogen activator, a complex eukaryotic protein harboring multiple disulfide bonds.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Robert B. Quast
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Rita Sachse
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Corina Schulze
- Beuth Hochschule für Technik Berlin - University of Applied Sciences Berlin, Life Sciences and Technology, Berlin, Germany
| | - Doreen A. Wüstenhagen
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
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