1
|
Zhang C, Chen S, Fu X, Dedkova LM, Hecht SM. Enhancement of N-Methyl Amino Acid Incorporation into Proteins and Peptides Using Modified Bacterial Ribosomes and Elongation Factor P. ACS Chem Biol 2024; 19:1330-1338. [PMID: 38769080 DOI: 10.1021/acschembio.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
N-Methylated amino acids are constituents of natural bioactive peptides and proteins. Nα-methylated amino acids appear abundantly in natural cyclic peptides, likely due to their constraint of peptide conformation and contribution to peptide stability. Peptides containing Nα-methylated amino acids have long been prepared by chemical synthesis. While such natural peptides are not produced ribosomally, recent ribosomal strategies have afforded Nα-methylated peptides. Presently, we define new strategies for the ribosomal incorporation of Nα-methylated amino acids into peptides and proteins. First, we identify modified ribosomes capable of facilitating the incorporation of six N-methylated amino acids into antibacterial scorpion peptide IsCT. Also synthesized analogously was a protein domain (RRM1) from hnRNP LL; improved yields were observed for nearly all tested N-methylated amino acids. Computational modeling of the ribosomal assembly illustrated how the distortion imposed by N-methylation could be compensated by altering the nucleotides in key 23S rRNA positions. Finally, it is known that incorporation of multiple prolines (an N-alkylated amino acid) ribosomally can be facilitated by bacterial elongation factor P. We report that supplementing endogenous EF-P during IsCT peptide and RRM1 protein synthesis gave improved yields for most of the N-methylated amino acids studied.
Collapse
Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xuan Fu
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
2
|
Matsumura R, Sato G, Kuruma Y. Protocol for in vitro phospholipid synthesis combining fatty acid synthesis and cell-free gene expression. STAR Protoc 2024; 5:103051. [PMID: 38700978 PMCID: PMC11078692 DOI: 10.1016/j.xpro.2024.103051] [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: 01/24/2024] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Phospholipids are important biomolecules for the study of lipidomics, signal transduction, biodiesel, and synthetic biology; however, it is difficult to synthesize and analyze phospholipids in a defined in vitro condition. Here, we present a protocol for in vitro production and quantification of phospholipids. We describe steps for preparing a cell-free system consisting of fatty acid synthesis and a gene expression system that synthesizes acyltransferases on liposomes. The whole reaction can be completed within a day and the products are quantified by liquid chromatography-mass spectrometry. For complete details on the use and execution of this protocol, please refer to Eto et al.1.
Collapse
Affiliation(s)
- Rumie Matsumura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho 2-15, Yokosuka 237-0061, Japan
| | - Gaku Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yutetsu Kuruma
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho 2-15, Yokosuka 237-0061, Japan.
| |
Collapse
|
3
|
Schoenmakers LLJ, den Uijl MJ, Postma JL, van den Akker TAP, Huck WTS, Driessen AJM. SecYEG-mediated translocation in a model synthetic cell. Synth Biol (Oxf) 2024; 9:ysae007. [PMID: 38807757 PMCID: PMC11131593 DOI: 10.1093/synbio/ysae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Giant unilamellar vesicles (GUVs) provide a powerful model compartment for synthetic cells. However, a key challenge is the incorporation of membrane proteins that allow for transport, energy transduction, compartment growth and division. Here, we have successfully incorporated the membrane protein complex SecYEG-the key bacterial translocase that is essential for the incorporation of newly synthesized membrane proteins-in GUVs. Our method consists of fusion of small unilamellar vesicles containing reconstituted SecYEG into GUVs, thereby forming SecGUVs. These are suitable for large-scale experiments while maintaining a high protein:lipid ratio. We demonstrate that incorporation of SecYEG into GUVs does not inhibit its translocation efficiency. Robust membrane protein functionalized proteo-GUVs are promising and flexible compartments for use in the formation and growth of synthetic cells.
Collapse
Affiliation(s)
- Ludo L J Schoenmakers
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Max J den Uijl
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jelle L Postma
- General Instrumentation, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Tim A P van den Akker
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Wilhelm T S Huck
- Physical-Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Arnold J M Driessen
- Groningen Biomolecular Sciences and Biotechnology, Molecular Biotechnology, University of Groningen, Groningen 9747 AG, The Netherlands
| |
Collapse
|
4
|
Hiroshima Y, Kido R, Kido JI, Bando M, Yoshida K, Murakami A, Shinohara Y. Synthesis of secretory leukocyte protease inhibitor using cell-free protein synthesis system. Odontology 2024:10.1007/s10266-024-00910-8. [PMID: 38502469 DOI: 10.1007/s10266-024-00910-8] [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: 10/10/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024]
Abstract
Secretory leukocyte protease inhibitor (SLPI) functions as a protease inhibitor that modulates excessive proteolysis in the body, exhibits broad-spectrum antimicrobial activity, regulates inflammatory responses, and plays an important role in the innate immunity. The purpose of the study was to artificially synthesize a SLPI, an antimicrobial peptide, and investigate its effect on antimicrobial activity against Porphyromonas gingivalis and interleukin-6 (IL-6) production. SLPI protein with a molecular weight of approximately 13 kDa was artificially synthesized using a cell-free protein synthesis (CFPS) system and investigated by western blotting and enzyme-linked immunosorbent assay (ELISA). Disulfide bond isomerase in the protein synthesis mixture increased the amount of SLPI synthesized. The synthesized SLPI (sSLPI) protein was purified and its antimicrobial activity was investigated based on the growth of Porphyromonas gingivalis and bacterial adhesion to oral epithelial cells. The effect of sSLPI on IL-6 production in human periodontal ligament fibroblasts (HPLFs) was examined by ELISA. Our results showed that sSLPI significantly inhibited the growth of Porphyromonas gingivalis and bacterial adhesion to oral epithelial cells and further inhibited IL-6 production by HPLFs. These results suggested that SLPI artificially synthesized using the CFPS system may play a role in the prevention of periodontal diseases through its antimicrobial and anti-inflammatory effects.
Collapse
Affiliation(s)
- Yuka Hiroshima
- Department of Oral Microbiology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan.
| | - Rie Kido
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Jun-Ichi Kido
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mika Bando
- Department of Periodontology and Endodontology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Promotion, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Akikazu Murakami
- Department of Oral Microbiology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| |
Collapse
|
5
|
Zhang X, Li P, Wang W, Zhao W, Dai S, Wang J, Li N, Dai Z. Self-lysis microbial consortia for predictable multi-proteins assembly. Bioorg Chem 2024; 144:107117. [PMID: 38266324 DOI: 10.1016/j.bioorg.2024.107117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/26/2024]
Abstract
The scope of bioengineering is expanding from the design of single strain to the microbial communities, allowing for the division-of-labor in synthesizing the multi-protein systems. Predicting the composition of the final product during the biomanufacturing process, however, can be difficult. Consortia-based manufacturing has the potential to boost production efficiency, but this benefit primarily holds in the upstream. The current format of downstream process heavily relies on the centralized facility, and is not economical and flexible to address the demands in small-scale. Here, we present a concise and manageable platform to enable the multi-protein system assembly. We engineer a self-lysis microbial consortium, where each strain lyses autonomously at high densities and produces a single protein component. The product fraction can be precisely tuned by varying the inoculation ratio. Utilizing this platform, we assemble a classical 34-component PURE (protein synthesis using recombinant elements) system. We have further optimized the downstream process of the biomanufacturing by incorporating the porous structure of polymeric materials. The encapsulated autolysis consortium can produce and release the proteins while maintaining the cell factories enclosed in the materials by exporting the multi-protein system for collection. Our research provides a novel approach to the flexible and controllable production of multi-protein systems, opening up new possibilities for pathway assembly and portable biomanufacturing.
Collapse
Affiliation(s)
- Xi Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pengcheng Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weijie Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenjuan Zhao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shengkun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jie Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Nan Li
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| |
Collapse
|
6
|
Hanafy MS, Cui Z. Connexin-Containing Vesicles for Drug Delivery. AAPS J 2024; 26:20. [PMID: 38267725 DOI: 10.1208/s12248-024-00889-8] [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: 09/30/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
Connexin is a transmembrane protein present on the cell membrane of most cell types. Connexins assemble into a hexameric hemichannel known as connexon that pairs with another hemichannel present on a neighboring cell to form gap junction that acts as a channel or pore for the transport of ions and small molecules between the cytoplasm of the two cells. Extracellular vesicles released from connexin-expressing cells could carry connexin hemichannels on their surface and couple with another connexin hemichannel on a distant recipient cell to allow the transfer of the intravesicular content directly into the cytoplasm. Connexin-containing vesicles can be potentially utilized for intracellular drug delivery. In this review, we introduced cell-derived, connexin-containing extracellular vesicles and cell-free connexin-containing liposomes, methods of preparing them, procedures to load cargos in them, factors regulating the connexin hemichannel activity, (potential) applications of connexin-containing vesicles in drug delivery, and finally the challenges and future directions in realizing the promises of this platform delivery system for (intracellular) drug delivery.
Collapse
Affiliation(s)
- Mahmoud S Hanafy
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA.
| |
Collapse
|
7
|
Schütz A, Bernhard F, Berrow N, Buyel JF, Ferreira-da-Silva F, Haustraete J, van den Heuvel J, Hoffmann JE, de Marco A, Peleg Y, Suppmann S, Unger T, Vanhoucke M, Witt S, Remans K. A concise guide to choosing suitable gene expression systems for recombinant protein production. STAR Protoc 2023; 4:102572. [PMID: 37917580 PMCID: PMC10643540 DOI: 10.1016/j.xpro.2023.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
Collapse
Affiliation(s)
- Anja Schütz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform for Protein Production & Characterization, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe-University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Johannes F Buyel
- Univeristy of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria
| | - Frederico Ferreira-da-Silva
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Jurgen Haustraete
- VIB, Center for Inflammation Research & Ugent, Department of Biomedical Molecular Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Joop van den Heuvel
- Helmholtz Centre for Infection Research (HZI), Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sabine Suppmann
- Protein Expression and Purification Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tamar Unger
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martine Vanhoucke
- BCCM/GeneCorner Plasmid Collection, Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Gent, Belgium
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Notkestr. 85, 22607 Hamburg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
8
|
Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. SMALL METHODS 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
Collapse
Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| |
Collapse
|
9
|
Goh MWS, Tozawa Y, Tero R. Assembly of Cell-Free Synthesized Ion Channel Molecules in Artificial Lipid Bilayer Observed by Atomic Force Microscopy. MEMBRANES 2023; 13:854. [PMID: 37999340 PMCID: PMC10673230 DOI: 10.3390/membranes13110854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Artificial lipid bilayer systems, such as vesicles, black membranes, and supported lipid bilayers (SLBs), are valuable platforms for studying ion channels at the molecular level. The reconstitution of the ion channels in an active form is a crucial process in studies using artificial lipid bilayer systems. In this study, we investigated the assembly of the human ether-a-go-go-related gene (hERG) channel prepared in a cell-free synthesis system. AFM topographies revealed the presence of protrusions with a uniform size in the entire SLB that was prepared with the proteoliposomes (PLs) incorporating the cell-free-synthesized hERG channel. We attributed the protrusions to hERG channel monomers, taking into consideration the AFM tip size, and identified assembled structures of the monomer that exhibited dimeric, trimeric, and tetrameric-like arrangements. We observed molecular images of the functional hERG channel reconstituted in a lipid bilayer membrane using AFM and quantitatively evaluated the association state of the cell-free synthesized hERG channel.
Collapse
Affiliation(s)
- Melvin Wei Shern Goh
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan;
| | - Ryugo Tero
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi 441-8580, Japan
| |
Collapse
|
10
|
Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
Collapse
Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| |
Collapse
|
11
|
Sato T, Matsuda S, Aoki W. Optimizing conditions to construct artificial cells using commercial in vitro transcription-translation system (PUREfrex2.0). J Biosci Bioeng 2023; 136:334-339. [PMID: 37517904 DOI: 10.1016/j.jbiosc.2023.07.004] [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: 05/08/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Artificial cells containing in vitro transcription and translation (IVTT) systems inside liposomes are important for the reconstruction and analysis of various biological systems. To improve the accessibility of artificial cell research, it is important that artificial cells can be constructed using only commercially available components. Here, we optimized the construction of artificial cells containing PUREfrex2.0, a commercially available IVTT with high transcriptional and translational activity. Specifically, the composition of the inner and outer s olutions of the liposomes and the concentrations of lipids, glucose/sucrose, potassium glutamate, and magnesium acetate were systematically optimized, and finally we found a protocol for the stable construction of artificial cells containing PUREfre×2.0. These findings are expected to be important in expanding the artificial cell research community.
Collapse
Affiliation(s)
- Toshiko Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | | | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
12
|
Liu Z, Chen S, Wu J. Advances in ultrahigh-throughput screening technologies for protein evolution. Trends Biotechnol 2023; 41:1168-1181. [PMID: 37088569 DOI: 10.1016/j.tibtech.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023]
Abstract
Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.
Collapse
Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China.
| |
Collapse
|
13
|
Levin R, Löhr F, Karakoc B, Lichtenecker R, Dötsch V, Bernhard F. E. coli "Stablelabel" S30 lysate for optimized cell-free NMR sample preparation. JOURNAL OF BIOMOLECULAR NMR 2023; 77:131-147. [PMID: 37311907 PMCID: PMC10406690 DOI: 10.1007/s10858-023-00417-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Cell-free (CF) synthesis with highly productive E. coli lysates is a convenient method to produce labeled proteins for NMR studies. Despite reduced metabolic activity in CF lysates, a certain scrambling of supplied isotope labels is still notable. Most problematic are conversions of 15N labels of the amino acids L-Asp, L-Asn, L-Gln, L-Glu and L-Ala, resulting in ambiguous NMR signals as well as in label dilution. Specific inhibitor cocktails suppress most undesired conversion reactions, while limited availability and potential side effects on CF system productivity need to be considered. As alternative route to address NMR label conversion in CF systems, we describe the generation of optimized E. coli lysates with reduced amino acid scrambling activity. Our strategy is based on the proteome blueprint of standardized CF S30 lysates of the E. coli strain A19. Identified lysate enzymes with suspected amino acid scrambling activity were eliminated by engineering corresponding single and cumulative chromosomal mutations in A19. CF lysates prepared from the mutants were analyzed for their CF protein synthesis efficiency and for residual scrambling activity. The A19 derivative "Stablelabel" containing the cumulative mutations asnA, ansA/B, glnA, aspC and ilvE yielded the most useful CF S30 lysates. We demonstrate the optimized NMR spectral complexity of selectively labeled proteins CF synthesized in "Stablelabel" lysates. By taking advantage of ilvE deletion in "Stablelabel", we further exemplify a new strategy for methyl group specific labeling of membrane proteins with the proton pump proteorhodopsin.
Collapse
Affiliation(s)
- Roman Levin
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Betül Karakoc
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
- MAG-LAB, 1030 Vienna, Austria
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| |
Collapse
|
14
|
Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
Collapse
Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| |
Collapse
|
15
|
Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
Collapse
Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
16
|
Mizuta R, Inoue F, Sasaki Y, Sawada SI, Akiyoshi K. A Facile Method to Coat Nanoparticles with Lipid Bilayer Membrane: Hybrid Silica Nanoparticles Disguised as Biomembrane Vesicles by Particle Penetration of Concentrated Lipid Layers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206153. [PMID: 36634998 DOI: 10.1002/smll.202206153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Natural membrane vesicles, including extracellular vesicles and enveloped viruses, participate in various events in vivo. To study and manipulate these events, biomembrane-coated nanoparticles inspired by natural membrane vesicles are developed. Herein, an efficient method is presented to prepare organic-inorganic hybrid materials in high yields that can accommodate various lipid compositions and particle sizes. To demonstrate this method, silica nanoparticles are passed through concentrated lipid layers prepared using density gradient centrifugation, followed by purification, to obtain lipid membrane-coated nanoparticles. Various lipids, including neutral, anionic, and cationic lipids, are used to prepare concentrated lipid layers. Single-particle analysis by imaging flow cytometry determines that silica nanoparticles are uniformly coated with a single lipid bilayer. Moreover, cellular uptake of silica nanoparticles is enhanced when covered with a lipid membrane containing cationic lipids. Finally, cell-free protein expression is applied to embed a membrane protein, namely the Spike protein of severe acute respiratory syndrome coronavirus 2, into the coating of the nanoparticles, with the correct orientation. Therefore, this method can be used to develop organic-inorganic hybrid nanomaterials with an inorganic core and a virus-like coating, serving as carriers for targeted delivery of cargos such as proteins, DNA, and drugs.
Collapse
Affiliation(s)
- Ryosuke Mizuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Fumihito Inoue
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Shin-Ichi Sawada
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, A3-317, Nishikyo-ku, Kyoto, 615-8510, Japan
| |
Collapse
|
17
|
Sihorwala AZ, Lin AJ, Stachowiak JC, Belardi B. Light-Activated Assembly of Connexon Nanopores in Synthetic Cells. J Am Chem Soc 2023; 145:3561-3568. [PMID: 36724060 PMCID: PMC10188233 DOI: 10.1021/jacs.2c12491] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During developmental processes and wound healing, activation of living cells occurs with spatiotemporal precision and leads to rapid release of soluble molecular signals, allowing communication and coordination between neighbors. Nonliving systems capable of similar responsive release hold great promise for information transfer in materials and site-specific drug delivery. One nonliving system that offers a tunable platform for programming release is synthetic cells. Encased in a lipid bilayer structure, synthetic cells can be outfitted with molecular conduits that span the bilayer and lead to material exchange. While previous work expressing membrane pore proteins in synthetic cells demonstrated content exchange, user-defined control over release has remained elusive. In mammalian cells, connexon nanopore structures drive content release and have garnered significant interest since they can direct material exchange through intercellular contacts. Here, we focus on connexon nanopores and present activated release of material from synthetic cells in a light-sensitive fashion. To do this, we re-engineer connexon nanopores to assemble after post-translational processing by a protease. By encapsulating proteases in light-sensitive liposomes, we show that assembly of nanopores can be triggered by illumination, resulting in rapid release of molecules encapsulated within synthetic cells. Controlling connexon nanopore activity provides an opportunity for initiating communication with extracellular signals and for transferring molecular agents to the cytoplasm of living cells in a rapid, light-guided manner.
Collapse
Affiliation(s)
- Ahmed Z Sihorwala
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander J Lin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
18
|
Tang C, Wang L, Zang L, Wang Q, Qi D, Dai Z. On-demand biomanufacturing through synthetic biology approach. Mater Today Bio 2022; 18:100518. [PMID: 36636637 PMCID: PMC9830231 DOI: 10.1016/j.mtbio.2022.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Biopharmaceuticals including protein therapeutics, engineered protein-based vaccines and monoclonal antibodies, are currently the mainstay products of the biotechnology industry. However, the need for specialized equipment and refrigeration during production and distribution poses challenges for the delivery of these technologies to the field and low-resource area. With the development of synthetic biology, multiple studies rewire the cell-free system or living cells to impact the portable, on-site and on-demand manufacturing of biomolecules. Here, we review these efforts and suggest future directions.
Collapse
Affiliation(s)
- Chenwang Tang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Lin Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lei Zang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qing Wang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Dianpeng Qi
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China,Corresponding author.
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China,Corresponding author.
| |
Collapse
|
19
|
Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
Collapse
Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
20
|
In vitro assembly, positioning and contraction of a division ring in minimal cells. Nat Commun 2022; 13:6098. [PMID: 36243816 PMCID: PMC9569390 DOI: 10.1038/s41467-022-33679-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023] Open
Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.
Collapse
|
21
|
Phospholipid synthesis inside phospholipid membrane vesicles. Commun Biol 2022; 5:1016. [PMID: 36167778 PMCID: PMC9515091 DOI: 10.1038/s42003-022-03999-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Construction of living artificial cells from genes and molecules can expand our understanding of life system and establish a new aspect of bioengineering. However, growth and division of cell membrane that are basis of cell proliferation are still difficult to reconstruct because a high-yielding phospholipid synthesis system has not been established. Here, we developed a cell-free phospholipid synthesis system that combines fatty acid synthesis and cell-free gene expression system synthesizing acyltransferases. The synthesized fatty acids were sequentially converted into phosphatidic acids by the cell-free synthesized acyltransferases. Because the system can avoid the accumulation of intermediates inhibiting lipid synthesis, sub-millimolar phospholipids could be synthesized within a single reaction mixture. We also performed phospholipid synthesis inside phospholipid membrane vesicles, which encapsulated all the components, and showed the phospholipids localized onto the mother membrane. Our approach would be a platform for the construction of self-reproducing artificial cells since the membrane can grow sustainably.
Collapse
|
22
|
Romantseva E, Alperovich N, Ross D, Lund SP, Strychalski EA. Effects of DNA template preparation on variability in cell-free protein production. Synth Biol (Oxf) 2022; 7:ysac015. [PMID: 36046152 PMCID: PMC9425043 DOI: 10.1093/synbio/ysac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/01/2022] [Accepted: 08/12/2022] [Indexed: 08/08/2023] Open
Abstract
DNA templates for protein production remain an unexplored source of variability in the performance of cell-free expression (CFE) systems. To characterize this variability, we investigated the effects of two common DNA extraction methodologies, a postprocessing step and manual versus automated preparation on protein production using CFE. We assess the concentration of the DNA template, the quality of the DNA template in terms of physical damage and the quality of the DNA solution in terms of purity resulting from eight DNA preparation workflows. We measure the variance in protein titer and rate of protein production in CFE reactions associated with the biological replicate of the DNA template, the technical replicate DNA solution prepared with the same workflow and the measurement replicate of nominally identical CFE reactions. We offer practical guidance for preparing and characterizing DNA templates to achieve acceptable variability in CFE performance.
Collapse
Affiliation(s)
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | - Steven P Lund
- National Institute of Standards and Technology, Gaithersburg, MD USA
| | | |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Lo CH, Zeng J. Application of polymersomes in membrane protein study and drug discovery: Progress, strategies, and perspectives. Bioeng Transl Med 2022; 8:e10350. [PMID: 36684106 PMCID: PMC9842050 DOI: 10.1002/btm2.10350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
Membrane proteins (MPs) play key roles in cellular signaling pathways and are responsible for intercellular and intracellular interactions. Dysfunctional MPs are directly related to the pathogenesis of various diseases, and they have been exploited as one of the most sought-after targets in the pharmaceutical industry. However, working with MPs is difficult given that their amphiphilic nature requires protection from biological membrane or membrane mimetics. Polymersomes are bilayered nano-vesicles made of self-assembled block copolymers that have been widely used as cell membrane mimetics for MP reconstitution and in engineering of artificial cells. This review highlights the prevailing trend in the application of polymersomes in MP study and drug discovery. We begin with a review on the techniques for synthesis and characterization of polymersomes as well as methods of MP insertion to form proteopolymersomes. Next, we review the structural and functional analysis of the different types of MPs reconstituted in polymersomes, including membrane transport proteins, MP complexes, and membrane receptors. We then summarize the factors affecting reconstitution efficiency and the quality of reconstituted MPs for structural and functional studies. Additionally, we discuss the potential in using proteopolymersomes as platforms for high-throughput screening (HTS) in drug discovery to identify modulators of MPs. We conclude by providing future perspectives and recommendations on advancing the study of MPs and drug development using proteopolymersomes.
Collapse
Affiliation(s)
- Chih Hung Lo
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore,Department of Neurology, Brigham and Women's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jialiu Zeng
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore,Department of Biomedical EngineeringBoston UniversityBostonMassachusettsUSA,Department of ChemistryBoston UniversityBostonMassachusettsUSA
| |
Collapse
|
25
|
Podolsky KA, Masubuchi T, Debelouchina GT, Hui E, Devaraj NK. In Situ Assembly of Transmembrane Proteins from Expressed and Synthetic Components in Giant Unilamellar Vesicles. ACS Chem Biol 2022; 17:1015-1021. [PMID: 35482050 PMCID: PMC9255206 DOI: 10.1021/acschembio.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituting functional transmembrane (TM) proteins into model membranes is challenging due to the difficulty of expressing hydrophobic TM domains, which often require stabilizing detergents that can perturb protein structure and function. Recent model systems solve this problem by linking the soluble domains of membrane proteins to lipids, using noncovalent conjugation. Herein, we test an alternative solution involving the in vitro assembly of TM proteins from synthetic TM domains and expressed soluble domains using chemoselective peptide ligation. We developed an intein mediated ligation strategy to semisynthesize single-pass TM proteins in synthetic giant unilamellar vesicle (GUV) membranes by covalently attaching soluble protein domains to a synthetic TM polypeptide, avoiding the requirement for detergent. We show that the extracellular domain of programmed cell death protein 1, a mammalian immune checkpoint receptor, retains its ligand-binding function at a membrane interface after ligation to a synthetic TM peptide in GUVs, facilitating the study of receptor-ligand interactions.
Collapse
Affiliation(s)
- K. A. Podolsky
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A
| | - T. Masubuchi
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, CA, U.S.A
| | - G. T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A
| | - E. Hui
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, CA, U.S.A
| | - N. K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, U.S.A.,Corresponding Author: Neal K. Devaraj,
| |
Collapse
|
26
|
Saito-Tarashima N, Murai A, Minakawa N. Rewriting the Central Dogma with Synthetic Genetic Polymers. Chem Pharm Bull (Tokyo) 2022; 70:310-315. [DOI: 10.1248/cpb.c21-00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Akiho Murai
- Graduate School of Pharmaceutical Science, Tokushima University
| | | |
Collapse
|
27
|
Protein folding in vitro and in the cell: From a solitary journey to a team effort. Biophys Chem 2022; 287:106821. [PMID: 35667131 PMCID: PMC9636488 DOI: 10.1016/j.bpc.2022.106821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
Abstract
Correct protein folding is essential for the health and function of living organisms. Yet, it is not well understood how unfolded proteins reach their native state and avoid aggregation, especially within the cellular milieu. Some proteins, especially small, single-domain and apparent two-state folders, successfully attain their native state upon dilution from denaturant. Yet, many more proteins undergo misfolding and aggregation during this process, in a concentration-dependent fashion. Once formed, native and aggregated states are often kinetically trapped relative to each other. Hence, the early stages of protein life are absolutely critical for proper kinetic channeling to the folded state and for long-term solubility and function. This review summarizes current knowledge on protein folding/aggregation mechanisms in buffered solution and within the bacterial cell, highlighting early stages. Remarkably, teamwork between nascent chain, ribosome, trigger factor and Hsp70 molecular chaperones enables all proteins to overcome aggregation propensities and reach a long-lived bioactive state.
Collapse
|
28
|
Berhanu S, Ueda T, Alix JH. The E. coli DnaK chaperone stimulates the α-complementation of β-galactosidase. J Basic Microbiol 2022; 62:669-688. [PMID: 35289419 DOI: 10.1002/jobm.202100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/20/2022] [Indexed: 11/09/2022]
Abstract
pUC18 and pUC19 are well-known high copy-number plasmid vectors routinely used for DNA cloning purposes. We show here that, in E. coli transformed by native pUC18, the α-complementation of β-galactosidase (i.e., mediated by the peptide LacZα18) is intrinsically weak and slow, but is greatly stimulated by the DnaK/DnaJ/GrpE chaperone system. In contrast, the α-complementation mediated by the peptide LacZα19 (in E. coli transformed by the native pUC19) is much more efficient, and therefore does not require the assistance of the DnaK chaperone machinery. The marked difference between these two LacZα peptides is reproduced in cell-free protein expression system coupled with α-complementation. We conclude that: (i) α-complementation of β-galactosidase is DnaK-mediated depending upon the LacZα peptide donor. (ii) DnaK, sensu stricto, is not necessary for α-complementation, but can enhance it to a great extent. (iii) this observation could be used to establish an easy and inexpensive method for screening small molecules libraries in search of DnaK inhibitors and also for deciphering the DnaK-mediated protein quality control mechanism. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Samuel Berhanu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Jean-Hervé Alix
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| |
Collapse
|
29
|
Blackholly LR, Harris NJ, Findlay HE, Booth PJ. Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein. Front Mol Biosci 2022; 9:795212. [PMID: 35187078 PMCID: PMC8847741 DOI: 10.3389/fmolb.2022.795212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/11/2022] [Indexed: 01/23/2023] Open
Abstract
The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.
Collapse
Affiliation(s)
| | | | | | - Paula J. Booth
- Department of Chemistry, King’s College London, London, United Kingdom
| |
Collapse
|
30
|
Romantseva EF, Tack DS, Alperovich N, Ross D, Strychalski EA. Best Practices for DNA Template Preparation Toward Improved Reproducibility in Cell-Free Protein Production. Methods Mol Biol 2022; 2433:3-50. [PMID: 34985735 DOI: 10.1007/978-1-0716-1998-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Performance variability is a common challenge in cell-free protein production and hinders a wider adoption of these systems for both research and biomanufacturing. While the inherent stochasticity and complexity of biology likely contributes to variability, other systematic factors may also play a role, including the source and preparation of the cell extract, the composition of the supplemental reaction buffer, the facility at which experiments are conducted, and the human operator (Cole et al. ACS Synth Biol 8:2080-2091, 2019). Variability in protein production could also arise from differences in the DNA template-specifically the amount of functional DNA added to a cell-free reaction and the quality of the DNA preparation in terms of contaminants and strand breakage. Here, we present protocols and suggest best practices optimized for DNA template preparation and quantitation for cell-free systems toward reducing variability in cell-free protein production.
Collapse
Affiliation(s)
| | - Drew S Tack
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | |
Collapse
|
31
|
Abstract
Hybrid membranes comprised of diblock copolymers, and phospholipids have gained interest due to their unique properties that result from blending natural and synthetic components. The integration of membrane proteins into these synthetic membranes is an important step towards creating biomembrane systems for uses such as artificial cellular systems, biosensors, and drug delivery vehicles. Here, we outline a technique to create hybrid membranes composed of phospholipids and diblock copolymers. Next, we describe how membrane proteins can be co-translationally integrated into hybrid lipid/polymer membranes using a cell-free reaction. We then outline a method to monitor insertion and folding of a membrane-embedded channel protein into the hybrid membrane using a fluorescent-protein reporter and dye release assay, respectively. This method is expected to be applicable for a wide range of membrane proteins that do not require chaperones for co-translational integration into vesicles and provides a generalized protocol for expressing a membrane protein into a membrane mimetic.
Collapse
Affiliation(s)
- Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, 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.
| |
Collapse
|
32
|
Altamura E, Albanese P, Mavelli F, Stano P. The Rise of the Nested Multicompartment Model in Synthetic Cell Research. Front Mol Biosci 2021; 8:750576. [PMID: 34540903 PMCID: PMC8446550 DOI: 10.3389/fmolb.2021.750576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
| | - Paola Albanese
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | - Fabio Mavelli
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| |
Collapse
|
33
|
Undabarrena A, Pereira CF, Kruasuwan W, Parra J, Sélem-Mojica N, Vind K, Schniete JK. Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001084. [PMID: 34515628 PMCID: PMC8549240 DOI: 10.1099/mic.0.001084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.
Collapse
Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Nelly Sélem-Mojica
- Centro de Ciencias Matemáticas, Antigua Carretera a Pátzcuaro # 8701, Col. Ex Hacienda San José de la Huerta, Morelia C.P. 58089, Michoacán, México
| | - Kristiina Vind
- NAICONS Srl, Viale Ortles 22/4, 20139 Milan (MI), Italy
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1 6708 WD, Wageningen, Netherlands
| | - Jana K. Schniete
- Biology, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
| |
Collapse
|
34
|
Leishmania tarentolae cell-free based approach for rapid anitbody-antigen interaction analysis. Methods Enzymol 2021; 659:391-409. [PMID: 34752297 DOI: 10.1016/bs.mie.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Rapid techniques for producing high-quality recombinant proteins are essential for fast protein functional analysis, as well as various screening applications. Cell-free protein expression is an enabling tool in protein research capable of producing high-quality proteins within a few hours. In this chapter, we describe the use of a Leishmania tarentolae-based cell-free expression system to produce antibody fragments coupled to the analysis of their interaction with their ligands. Interaction analysis is performed using the scalable and sensitive AlphaLISA bead proximity assay. The method presented in this chapter offers a rapid and inexpensive approach for production of putative interacting protein pairs, as well as a multiplexable approach for their rapid interaction analysis.
Collapse
|
35
|
Bhattacharya A, Cho CJ, Brea RJ, Devaraj NK. Expression of Fatty Acyl-CoA Ligase Drives One-Pot De Novo Synthesis of Membrane-Bound Vesicles in a Cell-Free Transcription-Translation System. J Am Chem Soc 2021; 143:11235-11242. [PMID: 34260248 DOI: 10.1021/jacs.1c05394] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the central importance of lipid membranes in cellular organization, it is challenging to reconstitute their formation de novo from minimal chemical and biological elements. Here, we describe a chemoenzymatic route to membrane-forming noncanonical phospholipids in which cysteine-modified lysolipids undergo spontaneous coupling with fatty acyl-CoA thioesters generated enzymatically by a fatty acyl-CoA ligase. Due to the high efficiency of the reaction, we were able to optimize phospholipid formation in a cell-free transcription-translation (TX-TL) system. Combining DNA encoding the fatty acyl-CoA ligase with suitable lipid precursors enabled one-pot de novo synthesis of membrane-bound vesicles. Noncanonical sphingolipid synthesis was also possible by using a cysteine-modified lysosphingomyelin as a precursor. When the sphingomyelin-interacting protein lysenin was coexpressed alongside the acyl-CoA ligase, the in situ assembled membranes were spontaneously decorated with protein. Our strategy of coupling gene expression with membrane lipid synthesis in a one-pot fashion could facilitate the generation of proteoliposomes and brings us closer to the bottom-up generation of synthetic cells using recombinant synthetic biology platforms.
Collapse
Affiliation(s)
- Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christy J Cho
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
36
|
Abstract
Lipid membranes in cells are fluid structures that undergo constant synthesis, remodeling, fission, and fusion. The dynamic nature of lipid membranes enables their use as adaptive compartments, making them indispensable for all life on Earth. Efforts to create life-like artificial cells will likely involve mimicking the structure and function of lipid membranes to recapitulate fundamental cellular processes such as growth and division. As such, there is considerable interest in chemistry that mimics the functional properties of membranes, with the express intent of recapitulating biological phenomena. We suggest expanding the definition of membrane mimetic chemistry to capture these efforts. In this Perspective, we discuss how membrane mimetic chemistry serves the development of artificial cells. By leveraging recent advances in chemical biology and systems chemistry, we have an opportunity to use simplified chemical and biochemical systems to mimic the remarkable properties of living membranes.
Collapse
Affiliation(s)
- Jacob A Vance
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
| | - Neal K Devaraj
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
| |
Collapse
|
37
|
Cotranslational recruitment of ribosomes in protocells recreates a translocon-independent mechanism of proteorhodopsin biogenesis. iScience 2021; 24:102429. [PMID: 33997704 PMCID: PMC8102411 DOI: 10.1016/j.isci.2021.102429] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 01/10/2023] Open
Abstract
The emergence of lipid membranes and embedded proteins was essential for the evolution of cells. Translocon complexes mediate cotranslational recruitment and membrane insertion of nascent proteins, but they already contain membrane-integral proteins. Therefore, a simpler mechanism must exist, enabling spontaneous membrane integration while preventing aggregation of unchaperoned protein in the aqueous phase. Here, we used giant unilamellar vesicles encapsulating minimal translation components to systematically interrogate the requirements for insertion of the model protein proteorhodopsin (PR) – a structurally ubiquitous membrane protein. We show that the N-terminal hydrophobic domain of PR is both necessary and sufficient for cotranslational recruitment of ribosomes to the membrane and subsequent membrane insertion of PR. Insertion of N-terminally truncated PR was restored by artificially attaching ribosomes to the membrane. Our findings offer a self-sufficient protein-inherent mechanism as a possible explanation for effective membrane protein biogenesis in a “pretranslocon” era, and they offer new opportunities for generating artificial cells. Generated a simple artificial cell model for membrane protein insertion We identified protein-inherent control of translational targeting without chaperones Ribosomes, artificially tethered to GUVs increased membrane protein insertion
Collapse
|
38
|
Kruyer NS, Sugianto W, Tickman BI, Alba Burbano D, Noireaux V, Carothers JM, Peralta-Yahya P. Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology. ACS Synth Biol 2021; 10:670-681. [PMID: 33749249 DOI: 10.1021/acssynbio.0c00625] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins are present in a wide array of cellular processes from primary and secondary metabolite synthesis to electron transport and single carbon metabolism. A key barrier to applying membrane proteins industrially is their difficult functional production. Beyond expression, folding, and membrane insertion, membrane protein activity is influenced by the physicochemical properties of the associated membrane, making it difficult to achieve optimal membrane protein performance outside the endogenous host. In this review, we highlight recent work on production of membrane proteins in membrane augmented cell-free systems (CFSs) and applications thereof. CFSs lack membranes and can thus be augmented with user-specified, tunable, mimetic membranes to generate customized environments for production of functional membrane proteins of interest. Membrane augmented CFSs would enable the synthesis of more complex plant secondary metabolites, the growth and division of synthetic cells for drug delivery and cell therapeutic applications, as well as enable green energy applications including methane capture and artificial photosynthesis.
Collapse
Affiliation(s)
- Nicholas S. Kruyer
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Widianti Sugianto
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Benjamin I. Tickman
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
| | - Diego Alba Burbano
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James M. Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Pamela Peralta-Yahya
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
39
|
Sun Q, Cao M, Zhang X, Wang M, Ma Y, Wang J. A simple and low-cost paper-based colorimetric method for detecting and distinguishing the GII.4 and GII.17 genotypes of norovirus. Talanta 2021; 225:121978. [PMID: 33592726 DOI: 10.1016/j.talanta.2020.121978] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022]
Abstract
In modern times, viruses still threaten people's lives. Among them, norovirus was the main pathogenic factor in the cause of gastroenteritis and foodborne illness, of which the GII.4 and GII.17 genotypes are prevalent in China and most parts of the world. A simple and low-cost platform for rapid and accurate norovirus detection remains a major challenge. After the cell-free system and paper-based chromogenic system were optimized, a rapid and specific norovirus detection method was established based on norovirus-specific sequences in combination with toehold switch elements. The development of a visible color change during detection eliminates the need for any complicated instruments. We validated this strategy and its specificity in differentiating GII.4, GII.17, Zika virus, and human coronavirus HKU1. The results showed that the optimized detection system not only provided a simple and rapid detection method for the sufficient differentiation of the two norovirus genotypes but also showed high specificity and no cross-reactivity with other viruses. Using nucleic acid isothermal amplification, this assay showed a limit of detection of 0.5 pM for the GII.4 genotype and 2.6 fM for the GII.17 genotype in reactions that could be observed directly with the naked eye. Our results suggested that this paper-based colorimetric method could serve as a simple and low-cost visual detection method for pathogens in clinical samples, especially in remote or rural areas.
Collapse
Affiliation(s)
- Qiuli Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Mengcen Cao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Meng Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| |
Collapse
|
40
|
Moore SJ, Lai HE, Chee SM, Toh M, Coode S, Chengan K, Capel P, Corre C, de los Santos ELC, Freemont PS. A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology. ACS Synth Biol 2021; 10:402-411. [PMID: 33497199 PMCID: PMC7901020 DOI: 10.1021/acssynbio.0c00581] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Prokaryotic
cell-free coupled transcription–translation
(TX-TL) systems are emerging as a powerful tool to examine natural
product biosynthetic pathways in a test tube. The key advantages of
this approach are the reduced experimental time scales and controlled
reaction conditions. To realize this potential, it is essential to
develop specialized cell-free systems in organisms enriched for biosynthetic
gene clusters. This requires strong protein production and well-characterized
synthetic biology tools. The Streptomyces genus is
a major source of natural products. To study enzymes and pathways
from Streptomyces, we originally developed a homologous Streptomyces cell-free system to provide a native protein
folding environment, a high G+C (%) tRNA pool, and an active background
metabolism. However, our initial yields were low (36 μg/mL)
and showed a high level of batch-to-batch variation. Here, we present
an updated high-yield and robust Streptomyces TX-TL
protocol, reaching up to yields of 266 μg/mL of expressed recombinant
protein. To complement this, we rapidly characterize a range of DNA
parts with different reporters, express high G+C (%) biosynthetic
genes, and demonstrate an initial proof of concept for combined transcription,
translation, and biosynthesis of Streptomyces metabolic
pathways in a single “one-pot” reaction.
Collapse
Affiliation(s)
- Simon J. Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Hung-En Lai
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Soo-Mei Chee
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ming Toh
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
| | - Seth Coode
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Kameshwari Chengan
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Patrick Capel
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Christophe Corre
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Emmanuel LC de los Santos
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Paul S. Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- Department Section of Structural and Synthetic Biology, Department of Infectious Disease; Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, U.K
- The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0N, U.K
| |
Collapse
|
41
|
Cell-Free Expression of a Plant Membrane Protein BrPT2 From Boesenbergia Rotunda. Mol Biotechnol 2021; 63:316-326. [PMID: 33565047 DOI: 10.1007/s12033-021-00304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Prenylation of aromatic natural products by membrane-bound prenyltransferases (PTs) is an important biosynthesis step of many bioactive compounds. At present, only a few plant flavonoid-related PT genes have been functionally characterized, mainly due to the difficulties of expressing these membrane proteins. Rapid and effective methods to produce functional plant membrane proteins are thus indispensable. Here, we evaluated expression systems through cell-based and cell-free approaches to express Boesenbergia rotunda BrPT2 encoding a membrane-bound prenyltransferase. We attempted to express BrPT2 in Escherichia coli and tobacco plants but failed to detect this protein using the Western-blot technique, whereas an intact single band of 43 kDa was detected when BrPT2 was expressed using a cell-free protein synthesis system (PURE). Under in vitro enzymatic condition, the synthesized BrPT2 successfully catalyzed pinostrobin chalcone to pinostrobin. Molecular docking analysis showed that pinostrobin chalcone interacts with BrPT2 at two cavities: (1) the main binding site at the central cavity and (2) the allosteric binding site located away from the central cavity. Our findings suggest that cell-free protein synthesis could be an alternative for rapid production of valuable difficult-to-express membrane proteins.
Collapse
|
42
|
Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| |
Collapse
|
43
|
Koo J, Yang J, Park H. Cell-free Systems: Recent Advances and Future Outlook. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
44
|
|
45
|
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]
|
46
|
Tarashima NS, Matsuo A, Minakawa N. Gene Expression of 4'-Thioguanine DNA via 4'-Thiocytosine RNA. J Am Chem Soc 2020; 142:17255-17259. [PMID: 33016701 DOI: 10.1021/jacs.0c07145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA and RNA nucleotides are ubiquitous molecules that store and transmit genetic information. The emergence of synthetic elements that fulfill the function of DNA and RNA provides an alternative gene expression system. Herein, we demonstrate the gene expression of 4'-thioguanine DNA (dSG DNA) via 4'-thiocytosine RNA (dSC RNA) to give green fluorescent protein (GFPuv) in a single test tube. In replication, transcription, and translation, DNA/RNA polymerases and Escherichia coli (E. coli) ribosome can tolerate the replacement of O4' with S4' in the nucleotide, despite the fact that sulfur has a larger atomic radius than oxygen. Additionally, dSG DNA and dSC RNA acted as alternative genetic polymers to natural DNA and RNA for protein synthesis in artificial cells comprising a reconstituted E. coli gene expression machinery. This work involved simple experiments that are widely used in molecular biology, but which underscore the feasibility of life control by substances other than DNA/RNA nucleotides.
Collapse
Affiliation(s)
- Noriko S Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
| | - Ayako Matsuo
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima, 770-8505, Japan
| |
Collapse
|
47
|
Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
Collapse
Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| |
Collapse
|
48
|
Toparlak ÖD, Zasso J, Bridi S, Serra MD, Macchi P, Conti L, Baudet ML, Mansy SS. Artificial cells drive neural differentiation. SCIENCE ADVANCES 2020; 6:eabb4920. [PMID: 32948587 PMCID: PMC7500934 DOI: 10.1126/sciadv.abb4920] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/29/2020] [Indexed: 05/02/2023]
Abstract
We report the construction of artificial cells that chemically communicate with mammalian cells under physiological conditions. The artificial cells respond to the presence of a small molecule in the environment by synthesizing and releasing a potent protein signal, brain-derived neurotrophic factor. Genetically controlled artificial cells communicate with engineered human embryonic kidney cells and murine neural stem cells. The data suggest that artificial cells are a versatile chassis for the in situ synthesis and on-demand release of chemical signals that elicit desired phenotypic changes of eukaryotic cells, including neuronal differentiation. In the future, artificial cells could be engineered to go beyond the capabilities of typical smart drug delivery vehicles by synthesizing and delivering specific therapeutic molecules tailored to distinct physiological conditions.
Collapse
Affiliation(s)
- Ö Duhan Toparlak
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Jacopo Zasso
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Simone Bridi
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Mauro Dalla Serra
- National Research Council-Institute of Biophysics & Bruno Kessler Foundation, via alla Cascata 56/C, 38123 Trento, Italy
| | - Paolo Macchi
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Marie-Laure Baudet
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy.
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| |
Collapse
|
49
|
Pellowe G, Findlay HE, Lee K, Gemeinhardt TM, Blackholly LR, Reading E, Booth PJ. Capturing Membrane Protein Ribosome Nascent Chain Complexes in a Native-like Environment for Co-translational Studies. Biochemistry 2020; 59:2764-2775. [PMID: 32627541 PMCID: PMC7551657 DOI: 10.1021/acs.biochem.0c00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Indexed: 01/02/2023]
Abstract
Co-translational folding studies of membrane proteins lag behind cytosolic protein investigations largely due to the technical difficulty in maintaining membrane lipid environments for correct protein folding. Stalled ribosome-bound nascent chain complexes (RNCs) can give snapshots of a nascent protein chain as it emerges from the ribosome during biosynthesis. Here, we demonstrate how SecM-facilitated nascent chain stalling and native nanodisc technologies can be exploited to capture in vivo-generated membrane protein RNCs within their native lipid compositions. We reveal that a polytopic membrane protein can be successfully stalled at various stages during its synthesis and the resulting RNC extracted within either detergent micelles or diisobutylene-maleic acid co-polymer native nanodiscs. Our approaches offer tractable solutions for the structural and biophysical interrogation of nascent membrane proteins of specified lengths, as the elongating nascent chain emerges from the ribosome and inserts into its native lipid milieu.
Collapse
Affiliation(s)
- Grant
A. Pellowe
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Heather E. Findlay
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Karen Lee
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Tim M. Gemeinhardt
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Laura R. Blackholly
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Eamonn Reading
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Paula J. Booth
- King’s College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| |
Collapse
|
50
|
Harris NJ, Pellowe GA, Booth PJ. Cell-free expression tools to study co-translational folding of alpha helical membrane transporters. Sci Rep 2020; 10:9125. [PMID: 32499529 PMCID: PMC7272624 DOI: 10.1038/s41598-020-66097-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 11/28/2022] Open
Abstract
Most helical membrane proteins fold co-translationally during unidirectional polypeptide elongation by the ribosome. Studies thus far, however, have largely focussed on refolding full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation offers opportunities to remedy this deficit in folding studies and has previously been used for membrane proteins. We exploit this cell-free approach to develop tools to probe co-translational folding. We show that two transporters from the ubiquitous Major Facilitator Superfamily can successfully insert into a synthetic bilayer without the need for translocon insertase apparatus that is essential in vivo. We also assess the cooperativity of domain insertion, by expressing the individual transporter domains cell-free. Furthermore, we manipulate the cell-free reaction to pause and re-start protein synthesis at specific points in the protein sequence. We find that full-length protein can still be made when stalling after the first N terminal helix has inserted into the bilayer. However, stalling after the first three helices have exited the ribosome cannot be successfully recovered. These three helices cannot insert stably when ribosome-bound during co-translational folding, as they require insertion of downstream helices.
Collapse
Affiliation(s)
- Nicola J Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Paula J Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
| |
Collapse
|